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Jirmanus LZ, Valenti RM, Griest Schwartzman EA, Simon-Ortiz SA, Frey LI, Friedman SR, Fullilove MT. Too Many Deaths, Too Many Left Behind: A People's External Review of the U.S. Centers for Disease Control and Prevention's COVID-19 Pandemic Response. AJPM FOCUS 2024; 3:100207. [PMID: 38770235 PMCID: PMC11103433 DOI: 10.1016/j.focus.2024.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The U.S. population has suffered worse health consequences owing to COVID-19 than comparable wealthy nations. COVID-19 had caused more than 1.1 million deaths in the U.S. as of May 2023 and contributed to a 3-year decline in life expectancy. A coalition of public health workers and community activists launched an external review of the Centers for Disease Control and Prevention's pandemic management from January 2021 to May 2023. The authors used a modified Delphi process to identify core pandemic management areas, which formed the basis for a survey and literature review. Their analysis yields 3 overarching shortcomings of the Centers for Disease Control and Prevention's pandemic management: (1) Centers for Disease Control and Prevention leadership downplays the serious impacts and aerosol transmission risks of COVID-19, (2) Centers for Disease Control and Prevention leadership has aligned public guidance with commercial and political interests over scientific evidence, and (3) Centers for Disease Control and Prevention guidance focuses on individual choice rather than emphasizing prevention and equity. Instead, the agency must partner with communities most impacted by the pandemic and encourage people to protect one another using layered protections to decrease COVID-19 transmission. Because emerging variants can already evade existing vaccines and treatments and Long COVID can be disabling and lacks definitive treatment, multifaceted, sustainable approaches to the COVID-19 pandemic are essential to protect people, the economy, and future generations.
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Affiliation(s)
- Lara Z. Jirmanus
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- People's CDC, Boston, Massachusetts
| | | | | | | | | | - Samuel R. Friedman
- People's CDC, Boston, Massachusetts
- Department of Population Health, NYU Grossman School of Medicine, New York, New York
- Center for Drug Use and HIV/HCV Research, NYU Grossman School of Public Health, New York, New York
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2
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Middleton C, Larremore DB. Modeling the transmission mitigation impact of testing for infectious diseases. SCIENCE ADVANCES 2024; 10:eadk5108. [PMID: 38875334 PMCID: PMC11177932 DOI: 10.1126/sciadv.adk5108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 05/10/2024] [Indexed: 06/16/2024]
Abstract
A fundamental question of any program focused on the testing and timely diagnosis of a communicable disease is its effectiveness in reducing transmission. Here, we introduce testing effectiveness (TE)-the fraction by which testing and post-diagnosis isolation reduce transmission at the population scale-and a model that incorporates test specifications and usage, within-host pathogen dynamics, and human behaviors to estimate TE. Using TE to guide recommendations, we show that today's rapid diagnostics should be used immediately upon symptom onset to control influenza A and respiratory syncytial virus but delayed by up to two days to control omicron-era severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Furthermore, while rapid tests are superior to reverse transcription quantitative polymerase chain reaction (RT-qPCR) to control founder-strain SARS-CoV-2, omicron-era changes in viral kinetics and rapid test sensitivity cause a reversal, with higher TE for RT-qPCR despite longer turnaround times. Last, we illustrate the model's flexibility by quantifying trade-offs in the use of post-diagnosis testing to shorten isolation times.
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Affiliation(s)
- Casey Middleton
- Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Daniel B. Larremore
- Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Santa Fe Institute, Santa Fe, NM, USA
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3
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Theel ES, Kirby JE, Pollock NR. Testing for SARS-CoV-2: lessons learned and current use cases. Clin Microbiol Rev 2024; 37:e0007223. [PMID: 38488364 DOI: 10.1128/cmr.00072-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
SUMMARYThe emergence and worldwide dissemination of SARS-CoV-2 required both urgent development of new diagnostic tests and expansion of diagnostic testing capacity on an unprecedented scale. The rapid evolution of technologies that allowed testing to move out of traditional laboratories and into point-of-care testing centers and the home transformed the diagnostic landscape. Four years later, with the end of the formal public health emergency but continued global circulation of the virus, it is important to take a fresh look at available SARS-CoV-2 testing technologies and consider how they should be used going forward. This review considers current use case scenarios for SARS-CoV-2 antigen, nucleic acid amplification, and immunologic tests, incorporating the latest evidence for analytical/clinical performance characteristics and advantages/limitations for each test type to inform current debates about how tests should or should not be used.
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Affiliation(s)
- Elitza S Theel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - James E Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R Pollock
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
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4
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Herbert C, Manabe YC, Filippaios A, Lin H, Wang B, Achenbach C, Kheterpal V, Hartin P, Suvarna T, Harman E, Stamegna P, Rao LV, Hafer N, Broach J, Luzuriaga K, Fitzgerald KA, McManus DD, Soni A. Differential Viral Dynamics by Sex and Body Mass Index During Acute SARS-CoV-2 Infection: Results From a Longitudinal Cohort Study. Clin Infect Dis 2024; 78:1185-1193. [PMID: 37972270 PMCID: PMC11093673 DOI: 10.1093/cid/ciad701] [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: 08/07/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND There is evidence of an association of severe coroanavirus disease (COVID-19) outcomes with increased body mass index (BMI) and male sex. However, few studies have examined the interaction between sex and BMI on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral dynamics. METHODS Participants conducted RT-PCR testing every 24-48 hours over a 15-day period. Sex and BMI were self-reported, and Ct values from E-gene were used to quantify viral load. Three distinct outcomes were examined using mixed-effects generalized linear models, linear models, and logistic models, respectively: all Ct values (model 1), nadir Ct value (model 2), and strongly detectable infection (at least 1 Ct value ≤28 during their infection) (model 3). An interaction term between BMI and sex was included, and inverse logit transformations were applied to quantify the differences by BMI and sex using marginal predictions. RESULTS In total, 7988 participants enrolled in this study and 439 participants (model 1) and 309 (models 2 and 3) were eligible for these analyses. Among males, increasing BMI was associated with lower Ct values in a dose-response fashion. For participants with BMIs greater than 29 kg/m2, males had significantly lower Ct values and nadir Ct values than females. In total, 67.8% of males and 55.3% of females recorded a strongly detectable infection; increasing proportions of men had Ct values <28 with BMIs of 35 and 40 kg/m2. CONCLUSIONS We observed sex-based dimorphism in relation to BMI and COVID-19 viral load. Further investigation is needed to determine the cause, clinical impact, and transmission implications of this sex-differential effect of BMI on viral load.
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Affiliation(s)
- Carly Herbert
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- UMass Center for Clinical and Translational Science, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Yukari C Manabe
- Division of Infectious Disease, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andreas Filippaios
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Honghuang Lin
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Biqi Wang
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Chad Achenbach
- Division of Infectious Disease, Department of Medicine, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | | | - Paul Hartin
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | | | | | - Pamela Stamegna
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | | | - Nathaniel Hafer
- UMass Center for Clinical and Translational Science, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - John Broach
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Katherine Luzuriaga
- UMass Center for Clinical and Translational Science, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Katherine A Fitzgerald
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - David D McManus
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Division of Cardiology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Apurv Soni
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- UMass Center for Clinical and Translational Science, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Division of Health System Science, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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5
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Esmaeili S, Owens K, Wagoner J, Polyak SJ, White JM, Schiffer JT. A unifying model to explain high nirmatrelvir therapeutic efficacy against SARS-CoV-2, despite low post-exposure prophylaxis efficacy and frequent viral rebound. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.08.23.23294505. [PMID: 38352583 PMCID: PMC10862980 DOI: 10.1101/2023.08.23.23294505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
In a pivotal trial (EPIC-HR), a 5-day course of oral ritonavir-boosted nirmatrelvir, given early during symptomatic SARS-CoV-2 infection (within three days of symptoms onset), decreased hospitalization and death by 89.1% and nasal viral load by 0.87 log relative to placebo in high-risk individuals. Yet, nirmatrelvir/ritonavir failed as post-exposure prophylaxis in a trial, and frequent viral rebound has been observed in subsequent cohorts. We developed a mathematical model capturing viral-immune dynamics and nirmatrelvir pharmacokinetics that recapitulated viral loads from this and another clinical trial (PLATCOV). Our results suggest that nirmatrelvir's in vivo potency is significantly lower than in vitro assays predict. According to our model, a maximally potent agent would reduce the viral load by approximately 3.5 logs relative to placebo at 5 days. The model identifies that earlier initiation and shorter treatment duration are key predictors of post-treatment rebound. Extension of treatment to 10 days for Omicron variant infection in vaccinated individuals, rather than increasing dose or dosing frequency, is predicted to lower the incidence of viral rebound significantly.
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Affiliation(s)
- Shadisadat Esmaeili
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, USA
| | - Katherine Owens
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, USA
| | - Jessica Wagoner
- Department of Medicine, University of Washington; Seattle, WA, USA
| | | | - Judith M. White
- Department of Cell Biology, University of Virginia; Charlottesville, VA, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, USA
- Department of Medicine, University of Washington; Seattle, WA, USA
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6
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Meyerowitz EA, Li Y. Review: The Landscape of Antiviral Therapy for COVID-19 in the Era of Widespread Population Immunity and Omicron-Lineage Viruses. Clin Infect Dis 2024; 78:908-917. [PMID: 37949817 DOI: 10.1093/cid/ciad685] [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: 09/11/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023] Open
Abstract
The goals of coronavirus disease 2019 (COVID-19) antiviral therapy early in the pandemic were to prevent severe disease, hospitalization, and death. As these outcomes have become infrequent in the age of widespread population immunity, the objectives have shifted. For the general population, COVID-19-directed antiviral therapy should decrease symptom severity and duration and minimize infectiousness, and for immunocompromised individuals, antiviral therapy should reduce severe outcomes and persistent infection. The increased recognition of virologic rebound following ritonavir-boosted nirmatrelvir (NMV/r) and the lack of randomized controlled trial data showing benefit of antiviral therapy for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection for standard-risk, vaccinated individuals remain major knowledge gaps. Here, we review data for selected antiviral agents and immunomodulators currently available or in late-stage clinical trials for use in outpatients. We do not review antibody products, convalescent plasma, systemic corticosteroids, IL-6 inhibitors, Janus kinase inhibitors, or agents that lack Food and Drug Administration approval or emergency use authorization or are not appropriate for outpatients.
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Affiliation(s)
- Eric A Meyerowitz
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center, Bronx, New York, USA
| | - Yijia Li
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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7
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Owens K, Esmaeili S, Schiffer JT. Heterogeneous SARS-CoV-2 kinetics due to variable timing and intensity of immune responses. JCI Insight 2024; 9:e176286. [PMID: 38573774 PMCID: PMC11141931 DOI: 10.1172/jci.insight.176286] [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: 09/29/2023] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
The viral kinetics of documented SARS-CoV-2 infections exhibit a high degree of interindividual variability. We identified 6 distinct viral shedding patterns, which differed according to peak viral load, duration, expansion rate, and clearance rate, by clustering data from 768 infections in the National Basketball Association cohort. Omicron variant infections in previously vaccinated individuals generally led to lower cumulative shedding levels of SARS-CoV-2 than other scenarios. We then developed a mechanistic mathematical model that recapitulated 1,510 observed viral trajectories, including viral rebound and cases of reinfection. Lower peak viral loads were explained by a more rapid and sustained transition of susceptible cells to a refractory state during infection as well as by an earlier and more potent late, cytolytic immune response. Our results suggest that viral elimination occurs more rapidly during Omicron infection, following vaccination, and following reinfection due to enhanced innate and acquired immune responses. Because viral load has been linked with COVID-19 severity and transmission risk, our model provides a framework for understanding the wide range of observed SARS-CoV-2 infection outcomes.
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Affiliation(s)
- Katherine Owens
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Shadisadat Esmaeili
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Joshua T. Schiffer
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
- University of Washington, Department of Medicine, Seattle, Washington, USA
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8
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Dietz E, Pritchard E, Pouwels K, Ehsaan M, Blake J, Gaughan C, Haduli E, Boothe H, Vihta KD, Peto T, Stoesser N, Matthews P, Taylor N, Diamond I, Studley R, Rourke E, Birrell P, De Angelis D, Fowler T, Watson C, Eyre D, House T, Walker AS. SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort. BMC Med 2024; 22:143. [PMID: 38532381 DOI: 10.1186/s12916-024-03351-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Syndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other respiratory viruses. METHODS We estimated the positivity and incidence of SARS-CoV-2, influenza A/B, and RSV, and trends in self-reported symptoms including influenza-like illness (ILI), over the 2022/23 winter season in a broadly representative UK community cohort (COVID-19 Infection Survey), using negative-binomial generalised additive models. We estimated associations between test positivity and each of the symptoms and influenza vaccination, using adjusted logistic and multinomial models. RESULTS Swabs taken at 32,937/1,352,979 (2.4%) assessments tested positive for SARS-CoV-2, 181/14,939 (1.2%) for RSV and 130/14,939 (0.9%) for influenza A/B, varying by age over time. Positivity and incidence peaks were earliest for RSV, then influenza A/B, then SARS-CoV-2, and were highest for RSV in the youngest and for SARS-CoV-2 in the oldest age groups. Many test positives did not report key symptoms: middle-aged participants were generally more symptomatic than older or younger participants, but still, only ~ 25% reported ILI-WHO and ~ 60% ILI-ECDC. Most symptomatic participants did not test positive for any of the three viruses. Influenza A/B-positivity was lower in participants reporting influenza vaccination in the current and previous seasons (odds ratio = 0.55 (95% CI 0.32, 0.95)) versus neither season. CONCLUSIONS Symptom profiles varied little by aetiology, making distinguishing SARS-CoV-2, influenza and RSV using symptoms challenging. Most symptoms were not explained by these viruses, indicating the importance of other pathogens in syndromic surveillance. Influenza vaccination was associated with lower rates of community influenza test positivity.
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Affiliation(s)
- Elisabeth Dietz
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK.
| | - Emma Pritchard
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
| | - Koen Pouwels
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Joshua Blake
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | | | - Eric Haduli
- Berkshire and Surrey Pathology Services, Camberley, UK
| | - Hugh Boothe
- Berkshire and Surrey Pathology Services, Camberley, UK
| | | | - Tim Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Philippa Matthews
- The Francis Crick Institute, 1 Midland Road, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | | | | | | | | | - Paul Birrell
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- UK Health Security Agency, London, UK
| | | | - Tom Fowler
- UK Health Security Agency, London, UK
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - David Eyre
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
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9
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Middleton C, Larremore DB. Modeling the Transmission Mitigation Impact of Testing for Infectious Diseases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.09.22.23295983. [PMID: 37808825 PMCID: PMC10557819 DOI: 10.1101/2023.09.22.23295983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
A fundamental question of any program focused on the testing and timely diagnosis of a communicable disease is its effectiveness in reducing transmission. Here, we introduce testing effectiveness (TE)-the fraction by which testing and post-diagnosis isolation reduce transmission at the population scale-and a model that incorporates test specifications and usage, within-host pathogen dynamics, and human behaviors to estimate TE. Using TE to guide recommendations, we show that today's rapid diagnostics should be used immediately upon symptom onset to control influenza A and respiratory syncytial virus (RSV), but delayed by up to 2d to control omicron-era SARS-CoV-2. Furthermore, while rapid tests are superior to RT-qPCR for control of founder-strain SARS-CoV-2, omicron-era changes in viral kinetics and rapid test sensitivity cause a reversal, with higher TE for RT-qPCR despite longer turnaround times. Finally, we illustrate the model's flexibility by quantifying tradeoffs in the use of post-diagnosis testing to shorten isolation times.
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Affiliation(s)
- Casey Middleton
- Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Daniel B Larremore
- Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Santa Fe Institute, Santa Fe, NM, USA
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10
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Eales O, Riley S. Differences between the true reproduction number and the apparent reproduction number of an epidemic time series. Epidemics 2024; 46:100742. [PMID: 38227994 DOI: 10.1016/j.epidem.2024.100742] [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: 07/10/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 01/18/2024] Open
Abstract
The time-varying reproduction number R(t) measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely known, and analysis of epidemics usually relies on time series data for other outcomes such as symptom onset. A common implicit assumption, when estimating R(t) from an epidemic time series, is that R(t) has the same relationship with these downstream outcomes as it does with the time series of incidence. However, this assumption is unlikely to be valid given that most epidemic time series are not perfect proxies of incidence. Rather they represent convolutions of incidence with uncertain delay distributions. Here we define the apparent time-varying reproduction number, RA(t), the reproduction number calculated from a downstream epidemic time series and demonstrate how differences between RA(t) and R(t) depend on the convolution function. The mean of the convolution function sets a time offset between the two signals, whilst the variance of the convolution function introduces a relative distortion between them. We present the convolution functions of epidemic time series that were available during the SARS-CoV-2 pandemic. Infection prevalence, measured by random sampling studies, presents fewer biases than other epidemic time series. Here we show that additionally the mean and variance of its convolution function were similar to that obtained from traditional surveillance based on mass-testing and could be reduced using more frequent testing, or by using stricter thresholds for positivity. Infection prevalence studies continue to be a versatile tool for tracking the temporal trends of R(t), and with additional refinements to their study protocol, will be of even greater utility during any future epidemics or pandemics.
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Affiliation(s)
- Oliver Eales
- Infectious Disease Dynamics Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia; School of Public Health, Imperial College London, London, United Kingdom; MRC Centre for Global infectious Disease Analysis, Imperial College London, London, United Kingdom; Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, United Kingdom.
| | - Steven Riley
- School of Public Health, Imperial College London, London, United Kingdom; MRC Centre for Global infectious Disease Analysis, Imperial College London, London, United Kingdom; Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, United Kingdom.
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11
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Tai CG, Haviland MJ, Kissler SM, Lucia RM, Merson M, Maragakis LL, Ho DD, Anderson DJ, DiFiori J, Grubaugh ND, Grad YH, Mack CD. Low antibody levels associated with significantly increased rate of SARS-CoV-2 infection in a highly vaccinated population from the US National Basketball Association. J Med Virol 2024; 96:e29505. [PMID: 38465748 DOI: 10.1002/jmv.29505] [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: 10/23/2023] [Revised: 02/12/2024] [Accepted: 02/23/2024] [Indexed: 03/12/2024]
Abstract
SARS-CoV-2 antibody levels may serve as a correlate for immunity and could inform optimal booster timing. The relationship between antibody levels and protection from infection was evaluated in vaccinated individuals from the US National Basketball Association who had antibody levels measured at a single time point from September 12, 2021, to December 31, 2021. Cox proportional hazards models were used to estimate the risk of infection within 90 days of serologic testing by antibody level (<250, 250-800, and >800 AU/mL1 ), adjusting for age, time since last vaccine dose, and history of SARS-CoV-2 infection. Individuals were censored on date of booster receipt. The analytic cohort comprised 2323 individuals and was 78.2% male, 68.1% aged ≤40 years, and 56.4% vaccinated (primary series) with the Pfizer-BioNTech mRNA vaccine. Among the 2248 (96.8%) individuals not yet boosted at antibody testing, 77% completed their primary vaccine series 4-6 months before testing and the median (interquartile range) antibody level was 293.5 (interquartile range: 121.0-740.5) AU/mL. Those with levels <250 AU/mL (adj hazard ratio [HR]: 2.4; 95% confidence interval [CI]: 1.5-3.7) and 250-800 AU/mL (adj HR: 1.5; 95% CI: 0.98-2.4) had greater infection risk compared to those with levels >800 AU/mL. Antibody levels could inform individual COVID-19 risk and booster scheduling.
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Affiliation(s)
| | | | - Steven M Kissler
- Harvard University T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Michael Merson
- Duke University Duke Global Health Institute, Durham, North Carolina, USA
| | - Lisa L Maragakis
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Deverick J Anderson
- Duke University Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, USA
| | - John DiFiori
- National Basketball Association, New York, New York, USA
- Hospital for Special Surgery, New York, New York, USA
| | - Nathan D Grubaugh
- Yale University School of Public Health, New Haven, Connecticut, USA
| | - Yonatan H Grad
- Harvard University T.H. Chan School of Public Health, Boston, Massachusetts, USA
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12
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Chevalier JM, Han AX, Hansen MA, Klock E, Pandithakoralage H, Ockhuisen T, Girdwood SJ, Lekodeba NA, de Nooy A, Khan S, Johnson CC, Sacks JA, Jenkins HE, Russell CA, Nichols BE. Impact and cost-effectiveness of SARS-CoV-2 self-testing strategies in schools: a multicountry modelling analysis. BMJ Open 2024; 14:e078674. [PMID: 38417953 PMCID: PMC10900377 DOI: 10.1136/bmjopen-2023-078674] [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: 08/09/2023] [Accepted: 02/13/2024] [Indexed: 03/01/2024] Open
Abstract
OBJECTIVES To determine the most epidemiologically effective and cost-effective school-based SARS-CoV-2 antigen-detection rapid diagnostic test (Ag-RDT) self-testing strategies among teachers and students. DESIGN Mathematical modelling and economic evaluation. SETTING AND PARTICIPANTS Simulated school and community populations were parameterised to Brazil, Georgia and Zambia, with SARS-CoV-2 self-testing strategies targeted to teachers and students in primary and secondary schools under varying epidemic conditions. INTERVENTIONS SARS-CoV-2 Ag-RDT self-testing strategies for only teachers or teachers and students-only symptomatically or symptomatically and asymptomatically at 5%, 10%, 40% or 100% of schools at varying frequencies. OUTCOME MEASURES Outcomes were assessed in terms of total infections and symptomatic days among teachers and students, as well as total infections and deaths within the community under the intervention compared with baseline. The incremental cost-effectiveness ratios (ICERs) were calculated for infections prevented among teachers and students. RESULTS With respect to both the reduction in infections and total cost, symptomatic testing of all teachers and students appears to be the most cost-effective strategy. Symptomatic testing can prevent up to 69·3%, 64·5% and 75·5% of school infections in Brazil, Georgia and Zambia, respectively, depending on the epidemic conditions, with additional reductions in community infections. ICERs for symptomatic testing range from US$2 to US$19 per additional school infection averted as compared with symptomatic testing of teachers alone. CONCLUSIONS Symptomatic testing of teachers and students has the potential to cost-effectively reduce a substantial number of school and community infections.
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Affiliation(s)
- Joshua M Chevalier
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Alvin X Han
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Megan A Hansen
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Ethan Klock
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Hiromi Pandithakoralage
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Tom Ockhuisen
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | | | - Nkgomeleng A Lekodeba
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Alexandra de Nooy
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | | | | | - Jilian A Sacks
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Helen E Jenkins
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Colin A Russell
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Brooke E Nichols
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
- FIND, Geneva, Switzerland
- Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
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13
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Frediani JK, Parsons R, McLendon KB, Westbrook AL, Lam W, Martin G, Pollock NR. The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs. Clin Infect Dis 2024; 78:301-307. [PMID: 37768707 PMCID: PMC10874267 DOI: 10.1093/cid/ciad582] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/11/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Early in the coronavirus disease 2019 (COVID-19) pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads. METHODS We assessed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A viral loads relative to symptom duration in symptomatic adults (≥16 years) presenting for testing in Georgia (4/2022-4/2023; Omicron variant predominant). Participants provided symptom duration and recent testing history. Nasal swabs were tested by Xpert Xpress SARS-CoV-2/Flu/RSV assay and cycle threshold (Ct) values recorded. Nucleoprotein concentrations in SARS-CoV-2 polymerase chain reaction (PCR)-positive samples were measured by single molecule array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated. RESULTS Of 348 newly-diagnosed SARS-CoV-2 PCR-positive individuals (65.5% women, median 39.2 years), 317/348 (91.1%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth/fifth day. Ag RDT sensitivity estimates were 30.0%-60.0% on the first day, 59.2%-74.8% on the third day, and 80.0%-93.3% on the fourth day of symptoms.In 74 influenza A PCR-positive individuals (55.4% women; median 35.0 years), median influenza viral loads peaked on the second day of symptoms. CONCLUSIONS In a highly immune adult population, median SARS-CoV-2 viral loads peaked around the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza.
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Affiliation(s)
- Jennifer K Frediani
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Richard Parsons
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Kaleb B McLendon
- Emory/Children's Laboratory for Innovative Assay Development, Department of Pathology, Emory University, Atlanta, Georgia, USA
| | - Adrianna L Westbrook
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Wilbur Lam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Greg Martin
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
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14
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Meyerowitz EA, Guha Roy S, Neilan AM, Ross DS, Mahowald GK. Case 5-2024: A 36-Year-Old Man with Fevers. N Engl J Med 2024; 390:653-660. [PMID: 38354145 DOI: 10.1056/nejmcpc2312724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Affiliation(s)
- Eric A Meyerowitz
- From the Department of Medicine, Montefiore Medical Center, and Albert Einstein College of Medicine - both in New York (E.A.M.); and the Departments of Radiology (S.G.R.), Pediatrics (A.M.N.), Medicine (A.M.N., D.S.R.), and Pathology (G.K.M.), Massachusetts General Hospital, and the Departments of Radiology (S.G.R.), Pediatrics (A.M.N.), Medicine (A.M.N., D.S.R.), and Pathology (G.K.M.), Harvard Medical School - both in Boston
| | - Shambo Guha Roy
- From the Department of Medicine, Montefiore Medical Center, and Albert Einstein College of Medicine - both in New York (E.A.M.); and the Departments of Radiology (S.G.R.), Pediatrics (A.M.N.), Medicine (A.M.N., D.S.R.), and Pathology (G.K.M.), Massachusetts General Hospital, and the Departments of Radiology (S.G.R.), Pediatrics (A.M.N.), Medicine (A.M.N., D.S.R.), and Pathology (G.K.M.), Harvard Medical School - both in Boston
| | - Anne M Neilan
- From the Department of Medicine, Montefiore Medical Center, and Albert Einstein College of Medicine - both in New York (E.A.M.); and the Departments of Radiology (S.G.R.), Pediatrics (A.M.N.), Medicine (A.M.N., D.S.R.), and Pathology (G.K.M.), Massachusetts General Hospital, and the Departments of Radiology (S.G.R.), Pediatrics (A.M.N.), Medicine (A.M.N., D.S.R.), and Pathology (G.K.M.), Harvard Medical School - both in Boston
| | - Douglas S Ross
- From the Department of Medicine, Montefiore Medical Center, and Albert Einstein College of Medicine - both in New York (E.A.M.); and the Departments of Radiology (S.G.R.), Pediatrics (A.M.N.), Medicine (A.M.N., D.S.R.), and Pathology (G.K.M.), Massachusetts General Hospital, and the Departments of Radiology (S.G.R.), Pediatrics (A.M.N.), Medicine (A.M.N., D.S.R.), and Pathology (G.K.M.), Harvard Medical School - both in Boston
| | - Grace K Mahowald
- From the Department of Medicine, Montefiore Medical Center, and Albert Einstein College of Medicine - both in New York (E.A.M.); and the Departments of Radiology (S.G.R.), Pediatrics (A.M.N.), Medicine (A.M.N., D.S.R.), and Pathology (G.K.M.), Massachusetts General Hospital, and the Departments of Radiology (S.G.R.), Pediatrics (A.M.N.), Medicine (A.M.N., D.S.R.), and Pathology (G.K.M.), Harvard Medical School - both in Boston
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15
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Owens K, Esmaeili-Wellman S, Schiffer JT. Heterogeneous SARS-CoV-2 kinetics due to variable timing and intensity of immune responses. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.08.20.23294350. [PMID: 37662228 PMCID: PMC10473815 DOI: 10.1101/2023.08.20.23294350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The viral kinetics of documented SARS-CoV-2 infections exhibit a high degree of inter-individual variability. We identified six distinct viral shedding patterns, which differed according to peak viral load, duration, expansion rate and clearance rate, by clustering data from 768 infections in the National Basketball Association cohort. Omicron variant infections in previously vaccinated individuals generally led to lower cumulative shedding levels of SARS-CoV-2 than other scenarios. We then developed a mechanistic mathematical model that recapitulated 1510 observed viral trajectories, including viral rebound and cases of reinfection. Lower peak viral loads were explained by a more rapid and sustained transition of susceptible cells to a refractory state during infection, as well as an earlier and more potent late, cytolytic immune response. Our results suggest that viral elimination occurs more rapidly during omicron infection, following vaccination, and following re-infection due to enhanced innate and acquired immune responses. Because viral load has been linked with COVID-19 severity and transmission risk, our model provides a framework for understanding the wide range of observed SARS-CoV-2 infection outcomes.
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Affiliation(s)
- Katherine Owens
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division
| | | | - Joshua T Schiffer
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division
- University of Washington, Department of Medicine
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16
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Ghafari M, Hall M, Golubchik T, Ayoubkhani D, House T, MacIntyre-Cockett G, Fryer HR, Thomson L, Nurtay A, Kemp SA, Ferretti L, Buck D, Green A, Trebes A, Piazza P, Lonie LJ, Studley R, Rourke E, Smith DL, Bashton M, Nelson A, Crown M, McCann C, Young GR, Santos RAND, Richards Z, Tariq MA, Cahuantzi R, Barrett J, Fraser C, Bonsall D, Walker AS, Lythgoe K. Prevalence of persistent SARS-CoV-2 in a large community surveillance study. Nature 2024; 626:1094-1101. [PMID: 38383783 PMCID: PMC10901734 DOI: 10.1038/s41586-024-07029-4] [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: 01/29/2023] [Accepted: 01/04/2024] [Indexed: 02/23/2024]
Abstract
Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks1-5, give rise to highly divergent lineages6-8 and contribute to cases with post-acute COVID-19 sequelae (long COVID)9,10. However, the population prevalence of persistent infections, their viral load kinetics and evolutionary dynamics over the course of infections remain largely unknown. Here, using viral sequence data collected as part of a national infection survey, we identified 381 individuals with SARS-CoV-2 RNA at high titre persisting for at least 30 days, of which 54 had viral RNA persisting at least 60 days. We refer to these as 'persistent infections' as available evidence suggests that they represent ongoing viral replication, although the persistence of non-replicating RNA cannot be ruled out in all. Individuals with persistent infection had more than 50% higher odds of self-reporting long COVID than individuals with non-persistent infection. We estimate that 0.1-0.5% of infections may become persistent with typically rebounding high viral loads and last for at least 60 days. In some individuals, we identified many viral amino acid substitutions, indicating periods of strong positive selection, whereas others had no consensus change in the sequences for prolonged periods, consistent with weak selection. Substitutions included mutations that are lineage defining for SARS-CoV-2 variants, at target sites for monoclonal antibodies and/or are commonly found in immunocompromised people11-14. This work has profound implications for understanding and characterizing SARS-CoV-2 infection, epidemiology and evolution.
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Affiliation(s)
- Mahan Ghafari
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Pandemic Science Institute, University of Oxford, Oxford, UK.
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Sydney Infectious Diseases Institute (Sydney ID), School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Daniel Ayoubkhani
- Office for National Statistics, Newport, UK
- Leicester Real World Evidence Unit, Diabetes Research Centre, University of Leicester, Leicester, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Helen R Fryer
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Laura Thomson
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - Anel Nurtay
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Steven A Kemp
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - Luca Ferretti
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - David Buck
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Angie Green
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Amy Trebes
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Lorne J Lonie
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | | | | | - Darren L Smith
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Andrew Nelson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Matthew Crown
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Clare McCann
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Gregory R Young
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Rui Andre Nunes Dos Santos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Zack Richards
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Mohammad Adnan Tariq
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | | | | | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - David Bonsall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, UK
| | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- MRC Clinical Trials Unit at UCL, UCL, London, UK
| | - Katrina Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Pandemic Science Institute, University of Oxford, Oxford, UK.
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17
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Aguilar Ticona JP, Xiao M, Li D, Nery N, Hitchings M, Belitardo EMMA, Fofana MO, Victoriano R, Cruz JS, de Moraes L, Strobel IM, Silva JJ, Sena do Aragão Filho A, Ribeiro GS, Reis MG, Costa F, Khouri R, Ko AI, Cummings DAT. Extensive transmission of SARS-CoV-2 BQ.1* variant in a population with high levels of hybrid immunity: A prevalence survey. Int J Infect Dis 2024; 139:159-167. [PMID: 38070701 PMCID: PMC10784150 DOI: 10.1016/j.ijid.2023.11.039] [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: 07/25/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 01/01/2024] Open
Abstract
OBJECTIVES The SARS-CoV-2 BQ.1* variant rapidly spread globally in late 2022, posing a challenge due to its increased immune evasion. METHODS We conducted a prevalence survey in Brazil from November 16 to December 22, 2022, as part of a cohort study. We conducted interviews and collected nasal samples for reverse transcription-polymerase chain reaction (RT-PCR) testing and whole-genome sequencing. Cumulative incidence was estimated using RT-PCR positivity, cycle threshold values, and external data on the dynamics of RT-PCR positivity following infection. RESULTS Among 535 participants, 54% had documented SARS-CoV-2 exposure before this outbreak and 74% had received COVID-19 vaccination. In this study, 14.8% tested positive for SARS-CoV-2, with BQ.1* identified in 90.7% of cases. Using case data and cycle threshold values, cumulative incidence was estimated at 56% (95% confidence interval, 36-88%). Of the 79 positive participants, 48.1% had a symptomatic illness, with a lower proportion fulfilling the World Health Organization COVID-19 case definition compared to prior Omicron waves. No participants required medical attention. CONCLUSIONS Despite high population-level hybrid immunity, the BQ.1* variant attacked 56% of our population. Lower disease severity was associated with BQ.1* compared to prior Omicron variants. Hybrid immunity may provide protection against future SARS-CoV-2 variants but in this case was not able to prevent widespread transmission.
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Affiliation(s)
- Juan P Aguilar Ticona
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil; Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States.
| | - Meng Xiao
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States; Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dan Li
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States; Public Health Emergency Center, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Nivison Nery
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil; Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States
| | - Matt Hitchings
- Department of Biostatistics, University of Florida, Gainesville, United States; Emerging Pathogens Institute, University of Florida, Gainesville, United States
| | | | - Mariam O Fofana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States
| | - Renato Victoriano
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
| | - Jaqueline S Cruz
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
| | - Laise de Moraes
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
| | - Icaro Morais Strobel
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
| | - Jessica Jesus Silva
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
| | | | - Guilherme S Ribeiro
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil; Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
| | - Mitermayer G Reis
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States; Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
| | - Federico Costa
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil; Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States
| | - Ricardo Khouri
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
| | - Albert I Ko
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States
| | - Derek A T Cummings
- Department of Biology, University of Florida, Gainesville, United States; Emerging Pathogens Institute, University of Florida, Gainesville, United States
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18
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Wang Q, Lu X, Jia R, Yan X, Wang J, Zhao L, Zhong R, Sun G. Recent advances in chemometric modelling of inhibitors against SARS-CoV-2. Heliyon 2024; 10:e24209. [PMID: 38293468 PMCID: PMC10826659 DOI: 10.1016/j.heliyon.2024.e24209] [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: 08/22/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused great harm to all countries worldwide. This disease can be prevented by vaccination and managed using various treatment methods, including injections, oral medications, or aerosol therapies. However, the selection of suitable compounds for the research and development of anti-SARS-CoV-2 drugs is a daunting task because of the vast databases of available compounds. The traditional process of drug research and development is time-consuming, labour-intensive, and costly. The application of chemometrics can significantly expedite drug R&D. This is particularly necessary and important for drug development against pandemic public emergency diseases, such as COVID-19. Through various chemometric techniques, such as quantitative structure-activity relationship (QSAR) modelling, molecular docking, and molecular dynamics (MD) simulations, compounds with inhibitory activity against SARS-CoV-2 can be quickly screened, allowing researchers to focus on the few prioritised candidates. In addition, the ADMET properties of the screened candidate compounds should be further explored to promote the successful discovery of anti-SARS-CoV-2 drugs. In this case, considerable time and economic costs can be saved while minimising the need for extensive animal experiments, in line with the 3R principles. This paper focuses on recent advances in chemometric modelling studies of COVID-19-related inhibitors, highlights current limitations, and outlines potential future directions for development.
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Affiliation(s)
- Qianqian Wang
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Xinyi Lu
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Runqing Jia
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Xinlong Yan
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Jianhua Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing 100124, PR China
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Guohui Sun
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
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19
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Lunt R, Quinot C, Kirsebom F, Andrews N, Skarnes C, Letley L, Haskins D, Angel C, Firminger S, Ratcliffe K, Rajan S, Sherridan A, Ijaz S, Zambon M, Brown K, Ramsay M, Bernal JL. The impact of vaccination and SARS-CoV-2 variants on the virological response to SARS-CoV-2 infections during the Alpha, Delta, and Omicron waves in England. J Infect 2024; 88:21-29. [PMID: 37926118 DOI: 10.1016/j.jinf.2023.10.016] [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: 05/31/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Vaccination status and the SARS-CoV-2 variant individuals are infected with are known to independently impact viral dynamics; however, little is known about the interaction of these two factors and how this impacts viral dynamics. Here we investigated how monovalent vaccination modified the time course and viral load of infections from different variants. Regression analyses were used to investigate the impact of vaccination on cycle threshold values and disease severity, and interval-censored survival analyses were used to investigate the impact of vaccination on duration of positivity. A range of covariates were adjusted for as potential confounders and investigated for their own effects in exploratory analyses. All analyses were done combining all variants and stratified by variant. For those infected with Alpha or Delta, vaccinated individuals were more likely to report mild disease than moderate/severe disease and had significantly shorter duration of positivity and lower viral loads compared to unvaccinated individuals. Vaccination had no impact on self-reported disease severity, viral load, or duration if positivity for those infected with Omicron. Overall, individuals who were immunosuppressed and clinically extremely vulnerable had longer duration of positivity and higher viral loads. This study adds to the evidence base on disease dynamics following COVID-19, demonstrating that vaccination mitigates severity of disease, the amount of detectable virus within infected individuals and reduces the time individuals are positive for. However, these effects have been significantly attenuated since the emergence of Omicron. Therefore, our findings strengthen the argument for using modified or multivalent vaccines that target emerging variants.
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Affiliation(s)
- Rachel Lunt
- UK Health Security Agency, London, United Kingdom.
| | | | | | - Nick Andrews
- UK Health Security Agency, London, United Kingdom; NIHR Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | | | | | | | | | | | | | - Samreen Ijaz
- UK Health Security Agency, London, United Kingdom
| | - Maria Zambon
- UK Health Security Agency, London, United Kingdom; NIHR Health Protection Research Unit in Respiratory Infections, Imperial College London, London, United Kingdom
| | - Kevin Brown
- UK Health Security Agency, London, United Kingdom
| | - Mary Ramsay
- UK Health Security Agency, London, United Kingdom; NIHR Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jamie Lopez Bernal
- UK Health Security Agency, London, United Kingdom; NIHR Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine, London, United Kingdom; NIHR Health Protection Research Unit in Respiratory Infections, Imperial College London, London, United Kingdom
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20
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Russell TW, Townsley H, Abbott S, Hellewell J, Carr EJ, Chapman LAC, Pung R, Quilty BJ, Hodgson D, Fowler AS, Adams L, Bailey C, Mears HV, Harvey R, Clayton B, O’Reilly N, Ngai Y, Nicod J, Gamblin S, Williams B, Gandhi S, Swanton C, Beale R, Bauer DLV, Wall EC, Kucharski AJ. Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants. PLoS Biol 2024; 22:e3002463. [PMID: 38289907 PMCID: PMC10826969 DOI: 10.1371/journal.pbio.3002463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 12/07/2023] [Indexed: 02/01/2024] Open
Abstract
The emergence of successive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) during 2020 to 2022, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics-such as varying levels of immunity-can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform Coronavirus Disease 2019 (COVID-19) planning and response and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both interindividual variation in Ct values and complex host characteristics-such as vaccination status, exposure history, and age-we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least 5 prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs. Trial Registration: The Legacy study is a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening for SARS-CoV-2 at University College London Hospitals or at the Francis Crick Institute (NCT04750356) (22,23). The Legacy study was approved by London Camden and Kings Cross Health Research Authority Research and Ethics committee (IRAS number 286469). The Legacy study was approved by London Camden and Kings Cross Health Research Authority Research and Ethics committee (IRAS number 286469) and is sponsored by University College London Hospitals. Written consent was given by all participants.
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Affiliation(s)
- Timothy W. Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Hermaleigh Townsley
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Sam Abbott
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Joel Hellewell
- European Molecular Biology Laboratory-European Bioinformatics Institute, Cambridge, United Kingdom
| | - Edward J. Carr
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Lloyd A. C. Chapman
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Lancaster University, Bailrigg, Lancaster, United Kingdom
| | - Rachael Pung
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Billy J. Quilty
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - David Hodgson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Lorin Adams
- The Francis Crick Institute, London, United Kingdom
| | - Chris Bailey
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | | | - Ruth Harvey
- The Francis Crick Institute, London, United Kingdom
| | | | | | - Yenting Ngai
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Jerome Nicod
- The Francis Crick Institute, London, United Kingdom
| | | | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- University College London, London, United Kingdom
| | - Sonia Gandhi
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Charles Swanton
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Rupert Beale
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK), London, United Kingdom
| | - David L. V. Bauer
- The Francis Crick Institute, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK), London, United Kingdom
| | - Emma C. Wall
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- University College London, London, United Kingdom
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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21
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Miyamoto S, Nishiyama T, Ueno A, Park H, Kanno T, Nakamura N, Ozono S, Aihara K, Takahashi K, Tsuchihashi Y, Ishikane M, Arashiro T, Saito S, Ainai A, Hirata Y, Iida S, Katano H, Tobiume M, Tokunaga K, Fujimoto T, Suzuki M, Nagashima M, Nakagawa H, Narita M, Kato Y, Igari H, Fujita K, Kato T, Hiyama K, Shindou K, Adachi T, Fukushima K, Nakamura-Uchiyama F, Hase R, Yoshimura Y, Yamato M, Nozaki Y, Ohmagari N, Suzuki M, Saito T, Iwami S, Suzuki T. Infectious virus shedding duration reflects secretory IgA antibody response latency after SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2023; 120:e2314808120. [PMID: 38134196 PMCID: PMC10756199 DOI: 10.1073/pnas.2314808120] [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: 08/26/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Infectious virus shedding from individuals infected with severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is used to estimate human-to-human transmission risk. Control of SARS-CoV-2 transmission requires identifying the immune correlates that protect infectious virus shedding. Mucosal immunity prevents infection by SARS-CoV-2, which replicates in the respiratory epithelium and spreads rapidly to other hosts. However, whether mucosal immunity prevents the shedding of the infectious virus in SARS-CoV-2-infected individuals is unknown. We examined the relationship between viral RNA shedding dynamics, duration of infectious virus shedding, and mucosal antibody responses during SARS-CoV-2 infection. Anti-spike secretory IgA antibodies (S-IgA) reduced viral RNA load and infectivity more than anti-spike IgG/IgA antibodies in infected nasopharyngeal samples. Compared with the IgG/IgA response, the anti-spike S-IgA post-infection responses affected the viral RNA shedding dynamics and predicted the duration of infectious virus shedding regardless of the immune history. These findings highlight the importance of anti-spike S-IgA responses in individuals infected with SARS-CoV-2 for preventing infectious virus shedding and SARS-CoV-2 transmission. Developing medical countermeasures to shorten S-IgA response time may help control human-to-human transmission of SARS-CoV-2 infection and prevent future respiratory virus pandemics.
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Affiliation(s)
- Sho Miyamoto
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Takara Nishiyama
- Interdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Aichi464-8602, Japan
| | - Akira Ueno
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Hyeongki Park
- Interdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Aichi464-8602, Japan
| | - Takayuki Kanno
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Naotoshi Nakamura
- Interdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Aichi464-8602, Japan
| | - Seiya Ozono
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, The University of Tokyo Institutes for Advanced Study, The University of Tokyo, Tokyo113-0033, Japan
| | - Kenichiro Takahashi
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Yuuki Tsuchihashi
- Center for surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo162-8640, Japan
- Center for Field Epidemic Intelligence, Research and Professional Development, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Masahiro Ishikane
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo162-8655, Japan
| | - Takeshi Arashiro
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
- Center for surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Shinji Saito
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Yuichiro Hirata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Harutaka Katano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Minoru Tobiume
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Kenzo Tokunaga
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Tsuguto Fujimoto
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Michiyo Suzuki
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo162-8655, Japan
| | - Maki Nagashima
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo162-8655, Japan
| | - Hidenori Nakagawa
- Department of Infectious Diseases, Osaka City General Hospital, Osaka534-0021, Japan
| | - Masashi Narita
- Division of Infectious Diseases, Department of Internal Medicine, Okinawa Prefectural Nanbu Medical Center and Children’s Medical Center, Okinawa901-1193, Japan
| | - Yasuyuki Kato
- Department of Infectious Diseases, International University of Health and Welfare Narita Hospital, Chiba286-0124, Japan
| | - Hidetoshi Igari
- Department of Infection Control, Chiba University Hospital, Chiba, Japan
| | - Kaori Fujita
- Department of Respiratory Medicine, National Hospital Organization Okinawa National Hospital, Okinawa901-2214, Japan
| | - Tatsuo Kato
- Department of Chest Disease, National Hospital Organization Nagara Medical Center, Gifu502-8558, Japan
| | - Kazutoshi Hiyama
- Department of Infectious Disease, National Hospital Organization Fukuoka-Higashi Medical Center, Fukuoka811-3195, Japan
| | - Keisuke Shindou
- Department of Pediatrics, Hirakata City Hospital, Osaka573-1013, Japan
| | - Takuya Adachi
- Department of Infectious Diseases, Tokyo Metropolitan Toshima Hospital, Tokyo173-0015, Japan
| | - Kazuaki Fukushima
- Department of Infectious Disease, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo113-8677, Japan
| | | | - Ryota Hase
- Department of Infectious Diseases, Japanese Red Cross Narita Hospital, Chiba286-8523, Japan
| | - Yukihiro Yoshimura
- Division of Infectious Disease, Yokohama Municipal Citizen’s Hospital, Kanagawa221-0855, Japan
| | - Masaya Yamato
- Department of General Internal Medicine and Infectious Diseases, Rinku General Medical Center 598-8577, Osaka, Japan
| | - Yasuhiro Nozaki
- Department of Respiratory Medicine, Tokoname City Hospital, Aichi479-8510, Japan
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo162-8655, Japan
| | - Motoi Suzuki
- Center for surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Tomoya Saito
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo162-8640, Japan
| | - Shingo Iwami
- Interdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Aichi464-8602, Japan
- Institute of Mathematics for Industry, Kyushu University, Fukuoka819-0395, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto606-8501, Japan
- Interdisciplinary Theoretical and Mathematical Sciences Program, RIKEN, Saitama351-0198, Japan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Science Groove Inc., Fukuoka810-0041, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo162-8640, Japan
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22
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Smith DJ, Lambrou A, Patel P. SARS-CoV-2 Rebound With and Without Use of COVID-19 Oral Antivirals. MMWR. MORBIDITY AND MORTALITY WEEKLY REPORT 2023; 72:1357-1364. [PMID: 38127665 PMCID: PMC10754268 DOI: 10.15585/mmwr.mm7251a1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Early treatment with a first-line therapy (nirmatrelvir/ritonavir [Paxlovid] or remdesivir) or second-line therapy (molnupiravir) prevents hospitalization and death among patients with mild-to-moderate COVID-19 who are at risk for severe disease and is recommended by the National Institutes of Health COVID-19 Treatment Guidelines. On May 25, 2023, the Food and Drug Administration approved nirmatrelvir/ritonavir for treatment of adults at high risk for severe disease. Although antiviral therapies are widely available, they are underutilized, possibly because of reports of SARS-CoV-2 rebound after treatment. To enhance current understanding of rebound, CDC reviewed SARS-CoV-2 rebound studies published during February 1, 2020- November 29, 2023. Overall, seven of 23 studies that met inclusion criteria, one randomized trial and six observational studies, compared rebound for persons who received antiviral treatment with that for persons who did not receive antiviral treatment. In four studies, including the randomized trial, no statistically significant difference in rebound rates was identified among persons receiving treatment and those not receiving treatment. Depending on the definition used, the prevalence of rebound varied. No hospitalizations or deaths were reported among outpatients who experienced rebound, because COVID-19 signs and symptoms were mild. Persons receiving antiviral treatment might be at higher risk for rebound compared with persons not receiving treatment because of host factors or treatment-induced viral suppression early in the course of illness. The potential for rebound should not deter clinicians from prescribing lifesaving antiviral treatments when indicated to prevent morbidity and mortality from COVID-19.
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23
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Nair MS, Luck MI, Huang Y, Sabo Y, Ho DD. Persistence of an infectious form of SARS-CoV-2 post protease inhibitor treatment of permissive cells in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572655. [PMID: 38187654 PMCID: PMC10769372 DOI: 10.1101/2023.12.20.572655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Reports have described SARS-CoV-2 rebound in COVID-19 patients treated with nirmatrelvir, a 3CL protease inhibitor. The cause remains a mystery, although drug resistance, re-infection, and lack of adequate immune responses have been excluded. We now present virologic findings that provide a clue to the cause of viral rebound, which occurs in ~20% of the treated cases. The persistence of an intermediary form of infectious SARS-CoV-2 was experimentally documented in vitro after treatment with nirmatrelvir or another 3CL protease inhibitor, but not with a polymerase inhibitor, remdesivir. This infectious intermediate decayed slowly with a half-life of ~1 day, suggesting that its persistence could outlive the treatment course to re-ignited SARS-CoV-2 infection as the drug is eliminated. Additional studies are needed to define the nature of this viral intermediate, but our findings point to a particular direction for future investigation and offer a specific treatment recommendation that should be tested clinically.
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Affiliation(s)
- Manoj S. Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Maria I. Luck
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yosef Sabo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Lead contact
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24
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Han AX, Hannay E, Carmona S, Rodriguez B, Nichols BE, Russell CA. Estimating the potential impact and diagnostic requirements for SARS-CoV-2 test-and-treat programs. Nat Commun 2023; 14:7981. [PMID: 38042923 PMCID: PMC10693634 DOI: 10.1038/s41467-023-43769-z] [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: 07/18/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023] Open
Abstract
Oral antivirals have the potential to reduce the public health burden of COVID-19. However, now that we have exited the emergency-phase of the COVID-19 pandemic, declining SARS-CoV-2 clinical testing rates (average testing rates = [Formula: see text]10 tests/100,000 people/day in low-and-middle income countries; <100 tests/100,000 people/day in high-income countries; September 2023) make the development of effective test-and-treat programs challenging. We used an agent-based model to investigate how testing rates and strategies affect the use and effectiveness of oral antiviral test-to-treat programs in four country archetypes of different income levels and demographies. We find that in the post-emergency-phase of the pandemic, in countries where low testing rates are driven by limited testing capacity, significant population-level impact of test-and-treat programs can only be achieved by both increasing testing rates and prioritizing individuals with greater risk of severe disease. However, for all countries, significant reductions in severe cases with antivirals are only possible if testing rates were substantially increased with high willingness of people to seek testing. Comparing the potential population-level reductions in severe disease outcomes of test-to-treat programs and vaccination shows that test-and-treat strategies are likely substantially more resource intensive requiring very high levels of testing (≫100 tests/100,000 people/day) and antiviral use suggesting that vaccination should be a higher priority.
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Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Emma Hannay
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Sergio Carmona
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Bill Rodriguez
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Brooke E Nichols
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
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25
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Rao A, Lin J, Parsons R, Greenleaf M, Westbrook A, Lai E, Bowers HB, McClendon K, O’Sick W, Baugh T, Sifford M, Sullivan JA, Lam WA, Bassit L. Standardization and Comparison of Emergency Use Authorized COVID-19 Assays and Testing Laboratories. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.08.23297633. [PMID: 37986832 PMCID: PMC10659510 DOI: 10.1101/2023.11.08.23297633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Motivation The motivation for this work was the need to establish a predefined cutoff based on genome copies per ml (GE/ml) rather than Ct, which can vary depending on the laboratory and assay used. A GE/ml-based threshold was necessary to define what constituted 'low positives" for samples that were included in data sets submitted to the FDA for emergency use approval for SARS-CoV-2 antigen tests. Summary SARS-CoV-2, the causal agent of the global COVID-19 pandemic, made its appearance at the end of 2019 and is still circulating in the population. The pandemic led to an urgent need for fast, reliable, and widely available testing. After December 2020, the emergence of new variants of SARS-CoV-2 led to additional challenges since new and existing tests had to detect variants to the same extent as the original Wuhan strain. When an antigen-based test is submitted to the Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) consideration it is benchmarked against PCR comparator assays, which yield cycle threshold (CT) data as an indirect indicator of viral load - the lower the CT, the higher the viral load of the sample and the higher the CT, the lower the viral load. The FDA mandates that 10-20% of clinical samples used to evaluate the antigen test have to be low positive. Low positive, as defined by the FDA, are clinical samples in which the CT of the SARS-CoV-2 target gene is within 3 CT of the mean CT value of the approved comparator test's Limit of Detection (LOD). While all comparator tests are PCR-based, the results from different PCR assays used are not uniform. Results vary depending on assay platform, target gene, LOD and laboratory methodology. The emergence and dominance of the Omicron variant further challenged this approach as the fraction of low positive clinical samples dramatically increased as compared to earlier SARS-CoV-2 variants. This led to 20-40% of clinical samples having high CT values and therefore assays vying for an EUA were failing to achieve the 80% Percent Positive Agreement (PPA) threshold required. Here we describe the methods and statistical analyses used to establish a predefined cutoff, based on genome copies per ml (GE/ml) to classify samples as low positive (less than the cutoff GE/ml) or high positive (greater than the cutoff GE/mL). CT 30 for the E gene target using Cobas® SARS-CoV-2-FluA/B platform performed at TriCore Reference Laboratories, and this low positive cutoff value was used for two EUA authorizations. Using droplet digital PCR and methods described here, a value 49,447.72 was determined as the GE/ml equivalent for the low positive cutoff. The CT cutoff corresponding to 49447.72 GE/ml was determined across other platforms and laboratories. The methodology and statistical analysis described here can now be used for standardization of all comparators used for FDA submissions with a goal towards establishing uniform criteria for EUA authorization.
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Affiliation(s)
- Anuradha Rao
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jessica Lin
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Richard Parsons
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA USA
| | - Morgan Greenleaf
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory University School of Medicine, Atlanta, GA, USA
| | - Adrianna Westbrook
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Eric Lai
- Personalized Science San Diego CA 05403 USA
| | - Heather B. Bowers
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, Georgia
| | - Kaleb McClendon
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - William O’Sick
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - Tyler Baugh
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - Markayla Sifford
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - Julie A. Sullivan
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Wilbur A. Lam
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center at Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Leda Bassit
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, Georgia
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26
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Rao A, Westbrook A, Bassit L, Parsons R, Fitts E, Greenleaf M, McLendon K, Sullivan JA, O’Sick W, Baugh T, Bowers HB, Frank F, Wang E, Le M, Frediani J, Roychoudhury P, Greninger AL, Jerris R, Pollock NR, Ortlund EA, Roback JD, Lam WA, Piantadosi A. Sensitivity of rapid antigen tests against SARS-CoV-2 Omicron and Delta variants. J Clin Microbiol 2023; 61:e0013823. [PMID: 37728336 PMCID: PMC10654096 DOI: 10.1128/jcm.00138-23] [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: 02/02/2023] [Accepted: 07/22/2023] [Indexed: 09/21/2023] Open
Abstract
Rapid antigen tests (RATs) have become an invaluable tool for combating the COVID-19 pandemic. However, concerns have been raised regarding the ability of existing RATs to effectively detect emerging SARS-CoV-2 variants. We compared the performance of 10 commercially available, emergency use authorized RATs against the Delta and Omicron SARS-CoV-2 variants using both individual patient and serially diluted pooled clinical samples. The RATs exhibited lower sensitivity for Omicron samples when using PCR cycle threshold (CT) value (a rough proxy for RNA concentration) as the comparator. Interestingly, however, they exhibited similar sensitivity for Omicron and Delta samples when using quantitative antigen concentration as the comparator. We further found that the Omicron samples had lower ratios of antigen to RNA, which offers a potential explanation for the apparent lower sensitivity of RATs for that variant when using C T value as a reference. Our findings underscore the complexity in assessing RAT performance against emerging variants and highlight the need for ongoing evaluation in the face of changing population immunity and virus evolution.
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Affiliation(s)
- Anuradha Rao
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Adrianna Westbrook
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Leda Bassit
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, Georgia, USA
| | - Richard Parsons
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Eric Fitts
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Morgan Greenleaf
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kaleb McLendon
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
| | - Julie A. Sullivan
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - William O’Sick
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
| | - Tyler Baugh
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
| | - Heather B. Bowers
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, Georgia, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ethan Wang
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Mimi Le
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jennifer Frediani
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | | | - Robert Jerris
- Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Eric A. Ortlund
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - John D. Roback
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
| | - Wilbur A. Lam
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center at Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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Hart WS, Park H, Jeong YD, Kim KS, Yoshimura R, Thompson RN, Iwami S. Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study. Proc Natl Acad Sci U S A 2023; 120:e2305451120. [PMID: 37788317 PMCID: PMC10576149 DOI: 10.1073/pnas.2305451120] [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: 04/13/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023] Open
Abstract
In the era of living with COVID-19, the risk of localised SARS-CoV-2 outbreaks remains. Here, we develop a multiscale modelling framework for estimating the local outbreak risk for a viral disease (the probability that a major outbreak results from a single case introduced into the population), accounting for within-host viral dynamics. Compared to population-level models previously used to estimate outbreak risks, our approach enables more detailed analysis of how the risk can be mitigated through pre-emptive interventions such as antigen testing. Considering SARS-CoV-2 as a case study, we quantify the within-host dynamics using data from individuals with omicron variant infections. We demonstrate that regular antigen testing reduces, but may not eliminate, the outbreak risk, depending on characteristics of local transmission. In our baseline analysis, daily antigen testing reduces the outbreak risk by 45% compared to a scenario without antigen testing. Additionally, we show that accounting for heterogeneity in within-host dynamics between individuals affects outbreak risk estimates and assessments of the impact of antigen testing. Our results therefore highlight important factors to consider when using multiscale models to design pre-emptive interventions against SARS-CoV-2 and other viruses.
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Affiliation(s)
- William S. Hart
- Mathematical Institute, University of Oxford, OxfordOX2 6GG, United Kingdom
- lnterdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya464-8602, Japan
| | - Hyeongki Park
- lnterdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya464-8602, Japan
| | - Yong Dam Jeong
- lnterdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya464-8602, Japan
- Department of Mathematics, Pusan National University, Busan46241, South Korea
| | - Kwang Su Kim
- lnterdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya464-8602, Japan
- Department of Scientific Computing, Pukyong National University, Busan48513, South Korea
| | - Raiki Yoshimura
- lnterdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya464-8602, Japan
| | - Robin N. Thompson
- Mathematical Institute, University of Oxford, OxfordOX2 6GG, United Kingdom
- Mathematics Institute, University of Warwick, CoventryCV4 7AL, United Kingdom
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, CoventryCV4 7AL, United Kingdom
| | - Shingo Iwami
- lnterdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya464-8602, Japan
- Institute of Mathematics for Industry, Kyushu University, Fukuoka819-0395, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto606-8501, Japan
- Interdisciplinary Theoretical and Mathematical Sciences Program, RIKEN, Saitama351-0198, Japan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Science Groove Inc., Fukuoka810-0041, Japan
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28
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Kissler SM, Hay JA, Fauver JR, Mack C, Tai CG, Anderson DJ, Ho DD, Grubaugh ND, Grad YH. Viral kinetics of sequential SARS-CoV-2 infections. Nat Commun 2023; 14:6206. [PMID: 37798265 PMCID: PMC10556125 DOI: 10.1038/s41467-023-41941-z] [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: 03/22/2023] [Accepted: 09/22/2023] [Indexed: 10/07/2023] Open
Abstract
The impact of a prior SARS-CoV-2 infection on the progression of subsequent infections has been unclear. Using a convenience sample of 94,812 longitudinal RT-qPCR measurements from anterior nares and oropharyngeal swabs, we identified 71 individuals with two well-sampled SARS-CoV-2 infections between March 11th, 2020, and July 28th, 2022. We compared the SARS-CoV-2 viral kinetics of first vs. second infections in this group, adjusting for viral variant, vaccination status, and age. Relative to first infections, second infections usually featured a faster clearance time. Furthermore, a person's relative (rank-order) viral clearance time, compared to others infected with the same variant, was roughly conserved across first and second infections, so that individuals who had a relatively fast clearance time in their first infection also tended to have a relatively fast clearance time in their second infection (Spearman correlation coefficient: 0.30, 95% credible interval (0.12, 0.46)). These findings provide evidence that, like vaccination, immunity from a prior SARS-CoV-2 infection shortens the duration of subsequent acute SARS-CoV-2 infections principally by reducing viral clearance time. Additionally, there appears to be an inherent element of the immune response, or some other host factor, that shapes a person's relative ability to clear SARS-CoV-2 infection that persists across sequential infections.
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Affiliation(s)
- Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - James A Hay
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Joseph R Fauver
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | - Deverick J Anderson
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, NC, USA
| | - David D Ho
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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Dreyer NA, Mack CD. Tactical Considerations for Designing Real-World Studies: Fit-for-Purpose Designs That Bridge Research and Practice. Pragmat Obs Res 2023; 14:101-110. [PMID: 37786592 PMCID: PMC10541678 DOI: 10.2147/por.s396024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023] Open
Abstract
Real-world evidence (RWE) is being used to provide information on diverse groups of patients who may be highly impacted by disease but are not typically studied in traditional randomized clinical trials (RCT) and to obtain insights from everyday care settings and real-world adherence to inform clinical practice. RWE is derived from so-called real-world data (RWD), ie, information generated by clinicians in the course of everyday patient care, and is sometimes coupled with systematic input from patients in the form of patient-reported outcomes or from wearable biosensors. Studies using RWD are conducted to evaluate how well medical interventions, services, and diagnostics perform under conditions of real-world use, and may include long-term follow-up. Here, we describe the main types of studies used to generate RWE and offer pointers for clinicians interested in study design and execution. Our tactical guidance addresses (1) opportunistic study designs, (2) considerations about representativeness of study participants, (3) expectations for transparency about data provenance, handling and quality assessments, and (4) considerations for strengthening studies using record linkage and/or randomization in pragmatic clinical trials. We also discuss likely sources of bias and suggest mitigation strategies. We see a future where clinical records - patient-generated data and other RWD - are brought together and harnessed by robust study design with efficient data capture and strong data curation. Traditional RCT will remain the mainstay of drug development, but RWE will play a growing role in clinical, regulatory, and payer decision-making. The most meaningful RWE will come from collaboration with astute clinicians with deep practice experience and questioning minds working closely with patients and researchers experienced in the development of RWE.
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Quirk GE, Schoenle MV, Peyton KL, Uhrlaub JL, Lau B, Burgess JL, Ellingson K, Beitel S, Romine J, Lutrick K, Fowlkes A, Britton A, Tyner HL, Caban-Martinez AJ, Naleway A, Gaglani M, Yoon S, Edwards L, Olsho L, Dake M, LaFleur BJ, Nikolich JŽ, Sprissler R, Worobey M, Bhattacharya D. Determinants of de novo B cell responses to drifted epitopes in post-vaccination SARS-CoV-2 infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295384. [PMID: 37745498 PMCID: PMC10516057 DOI: 10.1101/2023.09.12.23295384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Vaccine-induced immunity may impact subsequent de novo responses to drifted epitopes in SARS-CoV-2 variants, but this has been difficult to quantify due to the challenges in recruiting unvaccinated control groups whose first exposure to SARS-CoV-2 is a primary infection. Through local, statewide, and national SARS-CoV-2 testing programs, we were able to recruit cohorts of individuals who had recovered from either primary or post-vaccination infections by either the Delta or Omicron BA.1 variants. Regardless of variant, we observed greater Spike-specific and neutralizing antibody responses in post-vaccination infections than in those who were infected without prior vaccination. Through analysis of variant-specific memory B cells as markers of de novo responses, we observed that Delta and Omicron BA.1 infections led to a marked shift in immunodominance in which some drifted epitopes elicited minimal responses, even in primary infections. Prior immunity through vaccination had a small negative impact on these de novo responses, but this did not correlate with cross-reactive memory B cells, arguing against competitive inhibition of naïve B cells. We conclude that dampened de novo B cell responses against drifted epitopes are mostly a function of altered immunodominance hierarchies that are apparent even in primary infections, with a more modest contribution from pre-existing immunity, perhaps due to accelerated antigen clearance.
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Affiliation(s)
- Grace E Quirk
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Marta V Schoenle
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Kameron L Peyton
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Jennifer L Uhrlaub
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Branden Lau
- University of Arizona Genomics Core and the Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ, USA
| | - Jefferey L Burgess
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - Katherine Ellingson
- Department of Epidemiology and Biostatistics, Zuckerman College of Public Health, University of Arizona, Tucson
| | - Shawn Beitel
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - James Romine
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - Karen Lutrick
- College of Medicine-Tucson, University of Arizona, Tucson, Arizona, USA
| | - Ashley Fowlkes
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Amadea Britton
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Harmony L Tyner
- St. Luke's Regional Health Care System, Duluth, Minnesota, USA
| | | | - Allison Naleway
- Kaiser Permanente Northwest Center for Health Research, Portland, Oregon, USA
| | - Manjusha Gaglani
- Baylor Scott & White Health and Texas A&M University College of Medicine, Temple, Texas, USA
| | - Sarang Yoon
- Rocky Mountain Center for Occupational and Environmental Health, Department of Family and Preventive Medicine, University of Utah Health, Salt Lake City, Utah, USA
| | | | | | - Michael Dake
- Office of the Senior Vice-President for Health Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Janko Ž Nikolich
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
- University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Ryan Sprissler
- University of Arizona Genomics Core and the Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
- Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA
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31
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Ali KM, Rashid PMA, Ali AM, Tofiq AM, Salih GF, Dana OI, Rostam HM. Clinical outcomes and phylogenetic analysis in reflection with three predominant clades of SARS-CoV-2 variants. Eur J Clin Invest 2023; 53:e14004. [PMID: 37036255 DOI: 10.1111/eci.14004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 04/11/2023]
Abstract
BACKGROUND The pandemic of coronavirus disease 2019 (COVID-19) has a broad spectrum of clinical manifestations. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) undergoes continuous evolution, resulting in the emergence of several variants. Each variant has a different severity and mortality rate. MATERIALS AND METHODS In this study, 1174 COVID-19 patients were studied for mortality and severity over three SARS-CoV-2 predominating variant periods in 2021 and 2022 in Sulaimani Province, Iraq. In each period, a representative, variant virus was subjected to phylogenetic and molecular and clinical analysis. RESULTS Phylogenetic analysis revealed three SARS-CoV-2 variants, belonging to: Delta B.1.617.2, Omicron BA.1.17.2, and Omicron BA.5.6. The Delta variants showed more severe symptoms and a lower PCR-Ct value than Omicron variants regardless of gender, and only 4.3% of the cases were asymptomatic. The mortality rate was lower with Omicron (.5% for BA.5.2 and 1.3% for BA.1.17.2) compared with Delta variants (2.5%). The higher mortality rate with Delta variants was in males (2.84%), while that with Omicron BA1.17.2 and BA.5.2 was in females, 1.05% and .0%, respectively. Age group (≥70) years had the highest mortality rate; however, it was (.0%) in the age group (30-49) years with Omicron variants, compared with (.96%) in Delta variants. CONCLUSIONS There has been a surge in COVID-19 infection in the city due to the predominant lineages of SARS-CoV-2, B.1.617, Omicron BA.1.17.2 and Omicron BA.5.6, respectively. A higher PCR-Ct value and severity of the Delta variant over Omicron BA.1.17.2 and/or BA.5.2 variants were significantly correlated with a higher death rate in the same order.
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Affiliation(s)
- Kameran M Ali
- Medical Laboratory Technology Department, Kalar Technical College, Sulaimani Polytechnic University, Kalar, Iraq
| | - Peshnyar M A Rashid
- Medical Laboratory Science Department, Komar University of Science and Technology, Sulaimania, Iraq
| | - Ayad M Ali
- Department of Chemistry, University of Garmian, Kalar, Iraq
| | - Ahmed M Tofiq
- Department of Biology, College of Education, University of Garmian, Head of International Academic Relations (IRO), Kalar, Iraq
| | - Gaza F Salih
- Biology Department, College of Science, University of Sulaimani, Sulaimania, Iraq
| | - Omer I Dana
- College of Veterinary Medicine, University of Sulaimani, Sulaimani, Iraq
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32
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Kucharski AJ, Chung K, Aubry M, Teiti I, Teissier A, Richard V, Russell TW, Bos R, Olivier S, Cao-Lormeau VM. Real-time surveillance of international SARS-CoV-2 prevalence using systematic traveller arrival screening: An observational study. PLoS Med 2023; 20:e1004283. [PMID: 37683046 PMCID: PMC10516411 DOI: 10.1371/journal.pmed.1004283] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 09/22/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Effective Coronavirus Disease 2019 (COVID-19) response relies on good knowledge of population infection dynamics, but owing to under-ascertainment and delays in symptom-based reporting, obtaining reliable infection data has typically required large dedicated local population studies. Although many countries implemented Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) testing among travellers, it remains unclear how accurately arrival testing data can capture international patterns of infection, because those arrival testing data were rarely reported systematically, and predeparture testing was often in place as well, leading to nonrepresentative infection status among arrivals. METHODS AND FINDINGS In French Polynesia, testing data were reported systematically with enforced predeparture testing type and timing, making it possible to adjust for nonrepresentative infection status among arrivals. Combining statistical models of polymerase chain reaction (PCR) positivity with data on international travel protocols, we reconstructed estimates of prevalence at departure using only testing data from arrivals. We then applied this estimation approach to the United States of America and France, using data from over 220,000 tests from travellers arriving into French Polynesia between July 2020 and March 2022. We estimated a peak infection prevalence at departure of 2.1% (95% credible interval: 1.7, 2.6%) in France and 1% (95% CrI: 0.63, 1.4%) in the USA in late 2020/early 2021, with prevalence of 4.6% (95% CrI: 3.9, 5.2%) and 4.3% (95% CrI: 3.6, 5%), respectively, estimated for the Omicron BA.1 waves in early 2022. We found that our infection estimates were a leading indicator of later reported case dynamics, as well as being consistent with subsequent observed changes in seroprevalence over time. We did not have linked data on traveller demography or unbiased domestic infection estimates (e.g., from random community infection surveys) in the USA and France. However, our methodology would allow for the incorporation of prior data from additional sources if available in future. CONCLUSIONS As well as elucidating previously unmeasured infection dynamics in these countries, our analysis provides a proof-of-concept for scalable and accurate leading indicator of global infections during future pandemics.
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Affiliation(s)
- Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, French Polynesia
| | - Kiyojiken Chung
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, French Polynesia
| | - Maite Aubry
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, French Polynesia
| | - Iotefa Teiti
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, French Polynesia
| | - Anita Teissier
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, French Polynesia
| | - Vaea Richard
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, French Polynesia
| | - Timothy W. Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Raphaëlle Bos
- Clinical Laboratory, Institut Louis Malardé, Papeete, French Polynesia
| | - Sophie Olivier
- Clinical Laboratory, Institut Louis Malardé, Papeete, French Polynesia
| | - Van-Mai Cao-Lormeau
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, French Polynesia
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33
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Kliegr T, Jarkovský J, Jiřincová H, Kuchař J, Karel T, Chudán D, Vojíř S, Zavřel M, Šanca O, Tachezy R. Can variants, reinfection, symptoms and test types affect COVID-19 diagnostic performance? A large-scale retrospective study of AG-RDTs during circulation of Delta and Omicron variants, Czechia, December 2021 to February 2022. Euro Surveill 2023; 28:2200938. [PMID: 37733239 PMCID: PMC10515498 DOI: 10.2807/1560-7917.es.2023.28.38.2200938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/26/2023] [Indexed: 09/22/2023] Open
Abstract
BackgroundThe sensitivity and specificity of selected antigen detection rapid diagnostic tests (AG-RDTs) for SARS-CoV-2 were determined in the unvaccinated population when the Delta variant was circulating. Viral loads, dynamics, symptoms and tissue tropism differ between Omicron and Delta.AimWe aimed to compare AG-RDT sensitivity and specificity in selected subgroups during Omicron vs Delta circulation.MethodsWe retrospectively paired AG-RDT results with PCRs registered in Czechia's Information System for Infectious Diseases from 1 to 25 December 2021 (Delta, n = 20,121) and 20 January to 24 February 2022 (Omicron, n = 47,104).ResultsWhen confirmatory PCR was conducted on the same day as AG-RDT as a proxy for antigen testing close to peak viral load, the average sensitivity for Delta was 80.4% and for Omicron 81.4% (p < 0.05). Sensitivity in vaccinated individuals was lower for Omicron (OR = 0.94; 95% confidence interval (CI): 0.87-1.03), particularly in reinfections (OR = 0.83; 95% CI: 0.75-0.92). Saliva AG-RDT sensitivity was below average for both Delta (74.4%) and Omicron (78.4%). Tests on the European Union Category A list had higher sensitivity than tests in Category B. The highest sensitivity for Omicron (88.5%) was recorded for patients with loss of smell or taste, however, these symptoms were almost 10-fold less common than for Delta. The sensitivity of AG-RDTs performed on initially asymptomatic individuals done 1, 2 or 3 days before a positive PCR test was consistently lower for Omicron compared with Delta.ConclusionSensitivity for Omicron was lower in subgroups that may become more common if SARS-CoV-2 becomes an endemic virus.
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Affiliation(s)
- Tomáš Kliegr
- These authors contributed equally to this article and share the first authorship
- Department of Information and Knowledge Engineering, Faculty of Informatics and Statistics, Prague University of Economics and Business, Prague, Czechia
| | - Jiří Jarkovský
- These authors contributed equally to this article and share the first authorship
- Institute of Biostatistics and Analyses, Faculty of Medicine, Masaryk University, Brno, Czechia
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czechia
| | - Helena Jiřincová
- National Reference Laboratory for Influenza and Respiratory Viruses, National Institute of Public Health, Prague, Czechia
| | - Jaroslav Kuchař
- Department of Software Engineering, Faculty of Information Technology, Czech Technical University, Prague, Czechia
| | - Tomáš Karel
- Department of Statistics and Probability, Faculty of Informatics and Statistics, Prague University of Economics and Business, Prague, Czechia
| | - David Chudán
- Department of Information and Knowledge Engineering, Faculty of Informatics and Statistics, Prague University of Economics and Business, Prague, Czechia
| | - Stanislav Vojíř
- Department of Information and Knowledge Engineering, Faculty of Informatics and Statistics, Prague University of Economics and Business, Prague, Czechia
| | - Michal Zavřel
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czechia
| | - Ondřej Šanca
- Institute of Biostatistics and Analyses, Faculty of Medicine, Masaryk University, Brno, Czechia
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czechia
| | - Ruth Tachezy
- Department of Genetics and Microbiology, Faculty of Science-BIOCEV, Charles University, Prague, Czechia
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Moragas M, Golemba MD, Fernández MF, Palladino M, Gómez S, Borgnia D, Ruhle M, Arias A, Ruvinsky S, Bologna R, Mangano A. COVID-19 in immunocompromised children: comparison of SARS-CoV-2 viral load dynamics between the first and third waves. Braz J Microbiol 2023; 54:1859-1864. [PMID: 37258876 PMCID: PMC10232338 DOI: 10.1007/s42770-023-01009-y] [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: 03/16/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023] Open
Abstract
SARS-CoV-2 dynamics across different COVID-19 waves has been unclear in immunocompromised children. We aimed to compare the dynamics of SARS-CoV-2 RNA viral load (VL) during the first and third waves of COVID-19 in immunocompromised children. A retrospective and longitudinal cohort study was conducted in a pediatric referral hospital of Argentina. The study included 28 admitted immunocompromised children with laboratory confirmed SARS-CoV-2 infection. Thirteen acquired the infection during COVID-19 first wave (May to August 2020, group 1 (G1)) and fifteen in the third wave (January to March 2022, group 2 (G2)). RNA viral load measure and its dynamic reconstruction were performed in nasopharyngeal swabs by validated quantitative, real time RT-PCR, and linear mixed-effects model, respectively. Of the 28 children included, 54% were girls, most of them had hemato-oncological pathology (57%), and the median age was 8 years (interquartile range (IQR): 3-13). The dynamic of VL was similar in both groups (P = 0.148), starting from a level of 5.34 log10 copies/mL (95% confidence interval (CI): 4.47-6.21) in G1 and 5.79 log10 copies/mL (95% CI: 4.93-6.65) in G2. Then, VL decayed with a rate of 0.059 (95% CI: 0.038-0.080) and 0.088 (95% CI: 0.058-0.118) log10 copies/mL per day since diagnosis and fell below the limit of quantification at days 51 and 39 after diagnosis in G1 and G2, respectively. Our results evidenced a longer viral RNA persistence in immunocompromised pediatric patients and no difference in VL dynamic between COVID-19 first wave-attributed to ancestral infections-and third wave-attributed to Omicron infections.
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Affiliation(s)
- Matías Moragas
- Unidad de Virología y Epidemiología Molecular - CONICET, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina.
| | - Marcelo D Golemba
- Unidad de Virología y Epidemiología Molecular - CONICET, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - María F Fernández
- Unidad de Virología y Epidemiología Molecular - CONICET, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcela Palladino
- Unidad de Cuidados Intermedios y Moderados, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Sandra Gómez
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniela Borgnia
- Unidad de Virología y Epidemiología Molecular - CONICET, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Martín Ruhle
- Unidad de Virología y Epidemiología Molecular - CONICET, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana Arias
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Silvina Ruvinsky
- Coordinación de Investigación, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Rosa Bologna
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea Mangano
- Unidad de Virología y Epidemiología Molecular - CONICET, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Ciudad Autónoma de Buenos Aires, Argentina
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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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Kim JE, Choi H, Lee M, Lee CH. The effect of shortening the quarantine period and lifting the indoor mask mandate on the spread of COVID-19: a mathematical modeling approach. Front Public Health 2023; 11:1166528. [PMID: 37546304 PMCID: PMC10401846 DOI: 10.3389/fpubh.2023.1166528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023] Open
Abstract
In this paper, we present a mathematical model to assess the impact of reducing the quarantine period and lifting the indoor mask mandate on the spread of Coronavirus Disease 2019 (COVID-19) in Korea. The model incorporates important epidemiological parameters, such as transmission rates and mortality rates, to simulate the transmission of the virus under different scenarios. Our findings reveal that the impact of mask wearing fades in the long term, which highlights the crucial role of quarantine in controlling the spread of the disease. In addition, balancing the confirmed cases and costs, the lifting of mandatory indoor mask wearing is cost-effective; however, maintaining the quarantine period remains essential. A relationship between the disease transmission rate and vaccine efficiency was also apparent, with higher transmission rates leading to a greater impact of the vaccine efficiency. Moreover, our findings indicate that a higher disease transmission rate exacerbates the consequences of early quarantine release.
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Affiliation(s)
- Jung Eun Kim
- Department of Mathematics and Computer Science, Korea Science Academy of KAIST, Busan, Republic of Korea
| | - Heejin Choi
- Department of Mathematical Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Minji Lee
- Department of Mathematical Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Chang Hyeong Lee
- Department of Mathematical Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
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Wong CKH, Lau KTK, Au ICH, Lau EHY, Poon LLM, Hung IFN, Cowling BJ, Leung GM. Viral burden rebound in hospitalised patients with COVID-19 receiving oral antivirals in Hong Kong: a population-wide retrospective cohort study. THE LANCET. INFECTIOUS DISEASES 2023; 23:683-695. [PMID: 36796397 PMCID: PMC9949892 DOI: 10.1016/s1473-3099(22)00873-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/23/2022] [Accepted: 12/14/2022] [Indexed: 02/15/2023]
Abstract
BACKGROUND Viral rebound after nirmatrelvir-ritonavir treatment has implications for the clinical management and isolation of patients with COVID-19. We evaluated an unselected, population-wide cohort to identify the incidence of viral burden rebound and associated risk factors and clinical outcomes. METHODS We did a retrospective cohort study of hospitalised patients with a confirmed diagnosis of COVID-19 in Hong Kong, China, for an observation period from Feb 26 to July 3, 2022 (during the omicron BA.2.2 variant wave). Adult patients (age ≥18 years) admitted 3 days before or after a positive COVID-19 test were selected from medical records held by the Hospital Authority of Hong Kong. We included patients with non-oxygen-dependent COVID-19 at baseline receiving either molnupiravir (800 mg twice a day for 5 days), nirmatrelvir-ritonavir (nirmatrelvir 300 mg with ritonavir 100 mg twice a day for 5 days), or no oral antiviral treatment (control group). Viral burden rebound was defined as a reduction in cycle threshold (Ct) value (≥3) on quantitative RT-PCR test between two consecutive measurements, with such decrease sustained in an immediately subsequent Ct measurement (for those patients with ≥3 Ct measurements). Logistic regression models were used to identify prognostic factors for viral burden rebound, and to assess associations between viral burden rebound and a composite clinical outcome of mortality, intensive care unit admission, and invasive mechanical ventilation initiation, stratified by treatment group. FINDINGS We included 4592 hospitalised patients with non-oxygen-dependent COVID-19 (1998 [43·5%] women and 2594 [56·5%] men). During the omicron BA.2.2 wave, viral burden rebound occurred in 16 of 242 patients (6·6% [95% CI 4·1-10·5]) receiving nirmatrelvir-ritonavir, 27 of 563 (4·8% [3·3-6·9]) receiving molnupiravir, and 170 of 3787 (4·5% [3·9-5·2]) in the control group. The incidence of viral burden rebound did not differ significantly across the three groups. Immunocompromised status was associated with increased odds of viral burden rebound, regardless of antiviral treatment (nirmatrelvir-ritonavir: odds ratio [OR] 7·37 [95% CI 2·56-21·26], p=0·0002; molnupiravir: 3·05 [1·28-7·25], p=0·012; control: 2·21 [1·50-3·27], p<0·0001). Among patients receiving nirmatrelvir-ritonavir, the odds of viral burden rebound were higher in those aged 18-65 years (vs >65 years; 3·09 [1·00-9·53], p=0·050), those with high comorbidity burden (score >6 on the Charlson Comorbidity Index; 6·02 [2·09-17·38], p=0·0009), and those concomitantly taking corticosteroids (7·51 [1·67-33·82], p=0·0086); whereas the odds were lower in those who were not fully vaccinated (0·16 [0·04-0·67], p=0·012). In patients receiving molnupiravir, those aged 18-65 years (2·68 [1·09-6·58], p=0·032) or on concomitant corticosteroids (3·11 [1·23-7·82], p=0·016) had increased odds of viral burden rebound. We found no association between viral burden rebound and occurrence of the composite clinical outcome from day 5 of follow-up (nirmatrelvir-ritonavir: adjusted OR 1·90 [0·48-7·59], p=0·36; molnupiravir: 1·05 [0·39-2·84], p=0·92; control: 1·27 [0·89-1·80], p=0·18). INTERPRETATION Viral burden rebound rates are similar between patients with antiviral treatment and those without. Importantly, viral burden rebound was not associated with adverse clinical outcomes. FUNDING Health and Medical Research Fund, Health Bureau, The Government of the Hong Kong Special Administrative Region, China. TRANSLATION For the Chinese translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Carlos K H Wong
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Department of Family Medicine and Primary Care, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China.
| | - Kristy T K Lau
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ivan C H Au
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric H Y Lau
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China; WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Centre for Immunology and Infection, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China
| | - Ivan F N Hung
- Infectious Diseases Division, Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China; WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gabriel M Leung
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China; WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
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Russell TW, Townsley H, Abbott S, Hellewell J, Carr EJ, Chapman L, Pung R, Quilty BJ, Hodgson D, Fowler AS, Adams L, Bailey C, Mears HV, Harvey R, Clayton B, O’Reilly N, Ngai Y, Nicod J, Gamblin S, Williams B, Gandhi S, Swanton C, Beale R, Bauer DLV, Wall EC, Kucharski A. Within-host SARS-CoV-2 viral kinetics informed by complex life course exposures reveals different intrinsic properties of Omicron and Delta variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.17.23290105. [PMID: 37292842 PMCID: PMC10246130 DOI: 10.1101/2023.05.17.23290105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The emergence of successive SARS-CoV-2 variants of concern (VOC) during 2020-22, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics - such as varying levels of immunity - can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform COVID-19 planning and response, and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both inter-individual variation in Ct values and complex host characteristics - such as vaccination status, exposure history and age - we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least five prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs.
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Affiliation(s)
- Timothy W. Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Hermaleigh Townsley
- The Francis Crick Institute, 1 Midland Road, London, UK
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | - Sam Abbott
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Joel Hellewell
- European Molecular Biology Laboratory-European Bioinformatics Institute, Cambridge, UK
| | - Edward J Carr
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Lloyd Chapman
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Lancaster University, Bailrigg, Lancaster
| | - Rachael Pung
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Billy J. Quilty
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - David Hodgson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Lorin Adams
- The Francis Crick Institute, 1 Midland Road, London, UK
| | | | | | - Ruth Harvey
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Bobbi Clayton
- The Francis Crick Institute, 1 Midland Road, London, UK
| | | | - Yenting Ngai
- The Francis Crick Institute, 1 Midland Road, London, UK
- University College London, Gower Street, London
| | - Jerome Nicod
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Steve Gamblin
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
- University College London, Gower Street, London
| | - Sonia Gandhi
- The Francis Crick Institute, 1 Midland Road, London, UK
- University College London, Gower Street, London
| | - Charles Swanton
- The Francis Crick Institute, 1 Midland Road, London, UK
- University College London, Gower Street, London
| | - Rupert Beale
- The Francis Crick Institute, 1 Midland Road, London, UK
- University College London, Gower Street, London
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | - David LV Bauer
- The Francis Crick Institute, 1 Midland Road, London, UK
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | - Emma C Wall
- The Francis Crick Institute, 1 Midland Road, London, UK
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
- University College London, Gower Street, London
| | - Adam Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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Frediani JK, Parsons R, McLendon KB, Westbrook AL, Lam W, Martin G, Pollock NR. The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.09.23289735. [PMID: 37214887 PMCID: PMC10197800 DOI: 10.1101/2023.05.09.23289735] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Early in the COVID-19 pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads. Methods We assessed SARS-CoV-2 and influenza A viral loads relative to symptom duration in recently-tested adults. Symptomatic participants ≥16y presenting to testing sites in Georgia (4/2022-4/2023; Omicron variant predominant) provided symptom duration. Nasal swab samples were tested by the Xpert Xpress SARS-CoV-2/Flu/RSV assay and Ct values recorded. Nucleoprotein concentrations in SARS-CoV-2 PCR-positive samples were measured by Single Molecule Array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated. Results Of 621 SARS-CoV-2 PCR-positive individuals (64.1% women, median 40.9y), 556/621 (89.5%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth day. Ag RDT sensitivity estimates were 35.7-71.4% on the first day, 63.9-78.7% on the third day, and 78.6-90.6% on the fourth day of symptoms.In 74 influenza A PCR-positive individuals (55.4% women; median 35.0y), median influenza viral loads peaked on the second day of symptoms. Conclusions In a highly immune adult population, median SARS-CoV-2 viral loads peaked on the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza. Key Points In a highly immune adult population, median SARS-CoV-2 viral loads by cycle threshold and antigen measurements peaked on the fourth day of symptoms, with implications for testing practice. In contrast, viral loads for influenza A peaked soon after symptom onset.
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Affiliation(s)
| | - Richard Parsons
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA USA
| | - Kaleb B. McLendon
- Emory/Children’s Laboratory for Innovative Assay Development, Department of Pathology, Emory University, Atlanta, GA USA
| | - Adrianna L. Westbrook
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, GA USA
| | - Wilbur Lam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA USA
| | - Greg Martin
- Department of Medicine, Emory University School of Medicine, Atlanta, GA USA
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA USA
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Markov PV, Ghafari M, Beer M, Lythgoe K, Simmonds P, Stilianakis NI, Katzourakis A. The evolution of SARS-CoV-2. Nat Rev Microbiol 2023; 21:361-379. [PMID: 37020110 DOI: 10.1038/s41579-023-00878-2] [Citation(s) in RCA: 226] [Impact Index Per Article: 226.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly be inferred indirectly before, such as the emergence of variants with distinct phenotypes, for example transmissibility, severity and immune evasion. This Review explores the mechanisms that generate genetic variation in SARS-CoV-2, underlying the within-host and population-level processes that underpin these events. We examine the selective forces that likely drove the evolution of higher transmissibility and, in some cases, higher severity during the first year of the pandemic and the role of antigenic evolution during the second and third years, together with the implications of immune escape and reinfections, and the increasing evidence for and potential relevance of recombination. In order to understand how major lineages, such as variants of concern (VOCs), are generated, we contrast the evidence for the chronic infection model underlying the emergence of VOCs with the possibility of an animal reservoir playing a role in SARS-CoV-2 evolution, and conclude that the former is more likely. We evaluate uncertainties and outline scenarios for the possible future evolutionary trajectories of SARS-CoV-2.
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Affiliation(s)
- Peter V Markov
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
- London School of Hygiene & Tropical Medicine, University of London, London, UK.
| | - Mahan Ghafari
- Big Data Institute, University of Oxford, Oxford, UK
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nikolaos I Stilianakis
- European Commission, Joint Research Centre (JRC), Ispra, Italy
- Department of Biometry and Epidemiology, University of Erlangen-Nuremberg, Erlangen, Germany
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Abstract
SARS-CoV-2 viral load and detection of infectious virus in the respiratory tract are the two key parameters for estimating infectiousness. As shedding of infectious virus is required for onward transmission, understanding shedding characteristics is relevant for public health interventions. Viral shedding is influenced by biological characteristics of the virus, host factors and pre-existing immunity (previous infection or vaccination) of the infected individual. Although the process of human-to-human transmission is multifactorial, viral load substantially contributed to human-to-human transmission, with higher viral load posing a greater risk for onward transmission. Emerging SARS-CoV-2 variants of concern have further complicated the picture of virus shedding. As underlying immunity in the population through previous infection, vaccination or a combination of both has rapidly increased on a global scale after almost 3 years of the pandemic, viral shedding patterns have become more distinct from those of ancestral SARS-CoV-2. Understanding the factors and mechanisms that influence infectious virus shedding and the period during which individuals infected with SARS-CoV-2 are contagious is crucial to guide public health measures and limit transmission. Furthermore, diagnostic tools to demonstrate the presence of infectious virus from routine diagnostic specimens are needed.
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Affiliation(s)
- Olha Puhach
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benjamin Meyer
- Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Isabella Eckerle
- Department of 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.
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42
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Focosi D, McConnell S, Shoham S, Casadevall A, Maggi F, Antonelli G. Nirmatrelvir and COVID-19: development, pharmacokinetics, clinical efficacy, resistance, relapse, and pharmacoeconomics. Int J Antimicrob Agents 2023; 61:106708. [PMID: 36603694 DOI: 10.1016/j.ijantimicag.2022.106708] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
Nirmatrelvir/ritonavir (N/R) is one of the most effective antiviral drugs against SARS-CoV-2. The preclinical development, pharmacodynamics and pharmacokinetics of N/R are reviewed herein. Randomized clinical trials have been conducted exclusively with pre-Omicron variants of concern, but in vitro studies show that efficacy against all Omicron sublineages is preserved, as confirmed by post-marketing observational studies. Nevertheless, investigations of large viral genome repositories have shown that mutation in the main protease causing resistance to N/R are increasingly frequent. In addition, virological and clinical rebounds after N/R discontinuation have been reported in immunocompetent patients. This finding is of concern when translated to immunocompromised patients, in whom N/R efficacy has not been formally investigated in clinical trials. Economical sustainability and perspectives for this therapeutic arena are discussed.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy.
| | - Scott McConnell
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
| | - Shmuel Shoham
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
| | - Arturo Casadevall
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases "Spallanzani", Rome, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, Sapienza University of Rome, and Sapienza University Hospital "Policlinico Umberto I", Rome, Italy
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43
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Nielsen SS, Alvarez J, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin M, Michel V, Miranda Chueca MÁ, Padalino B, Pasquali P, Roberts HC, Spoolder H, Velarde A, Viltrop A, Winckler C, Adlhoch C, Aznar I, Baldinelli F, Boklund A, Broglia A, Gerhards N, Mur L, Nannapaneni P, Ståhl K. SARS-CoV-2 in animals: susceptibility of animal species, risk for animal and public health, monitoring, prevention and control. EFSA J 2023; 21:e07822. [PMID: 36860662 PMCID: PMC9968901 DOI: 10.2903/j.efsa.2023.7822] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
The epidemiological situation of SARS-CoV-2 in humans and animals is continually evolving. To date, animal species known to transmit SARS-CoV-2 are American mink, raccoon dog, cat, ferret, hamster, house mouse, Egyptian fruit bat, deer mouse and white-tailed deer. Among farmed animals, American mink have the highest likelihood to become infected from humans or animals and further transmit SARS-CoV-2. In the EU, 44 outbreaks were reported in 2021 in mink farms in seven MSs, while only six in 2022 in two MSs, thus representing a decreasing trend. The introduction of SARS-CoV-2 into mink farms is usually via infected humans; this can be controlled by systematically testing people entering farms and adequate biosecurity. The current most appropriate monitoring approach for mink is the outbreak confirmation based on suspicion, testing dead or clinically sick animals in case of increased mortality or positive farm personnel and the genomic surveillance of virus variants. The genomic analysis of SARS-CoV-2 showed mink-specific clusters with a potential to spill back into the human population. Among companion animals, cats, ferrets and hamsters are those at highest risk of SARS-CoV-2 infection, which most likely originates from an infected human, and which has no or very low impact on virus circulation in the human population. Among wild animals (including zoo animals), mostly carnivores, great apes and white-tailed deer have been reported to be naturally infected by SARS-CoV-2. In the EU, no cases of infected wildlife have been reported so far. Proper disposal of human waste is advised to reduce the risks of spill-over of SARS-CoV-2 to wildlife. Furthermore, contact with wildlife, especially if sick or dead, should be minimised. No specific monitoring for wildlife is recommended apart from testing hunter-harvested animals with clinical signs or found-dead. Bats should be monitored as a natural host of many coronaviruses.
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Zheng W, Deng X, Peng C, Yan X, Zheng N, Chen Z, Yang J, Ajelli M, Zhang J, Yu H. Risk Factors Associated with the Spatiotemporal Spread of the SARS-CoV-2 Omicron BA.2 Variant — Shanghai Municipality, China, 2022. China CDC Wkly 2023; 5:97-102. [PMID: 37006708 PMCID: PMC10061774 DOI: 10.46234/ccdcw2023.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
What is already known about this topic? Previous studies have explored the spatial transmission patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and have assessed the associated risk factors. However, none of these studies have quantitatively described the spatiotemporal transmission patterns and risk factors for Omicron BA.2 at the micro (within-city) scale. What is added by this report? This study highlights the heterogeneous spread of the 2022 Omicron BA.2 epidemic in Shanghai, and identifies associations between different metrics of spatial spread at the subdistrict level and demographic and socioeconomic characteristics of the population, human mobility patterns, and adopted interventions. What are the implications for public health practice? Disentangling different risk factors might contribute to a deeper understanding of the transmission dynamics and ecology of coronavirus disease 2019 and an effective design of monitoring and management strategies.
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Affiliation(s)
- Wen Zheng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai Municipality, China
| | - Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai Municipality, China
| | - Cheng Peng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai Municipality, China
| | - Xuemei Yan
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai Municipality, China
| | - Nan Zheng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai Municipality, China
| | - Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai Municipality, China
| | - Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai Municipality, China
| | - Marco Ajelli
- Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai Municipality, China
- Juanjuan Zhang,
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai Municipality, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai Municipality, China
- Hongjie Yu,
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45
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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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Panorama of Breakthrough Infection Caused by SARS-CoV-2: A Review. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58121733. [PMID: 36556935 PMCID: PMC9784755 DOI: 10.3390/medicina58121733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
Since the outbreak of the novel coronavirus disease 2019 (COVID-19) in 2019, many countries have successively developed a variety of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, with the continuous spread of SARS-CoV-2, it has evolved several variants; as a result, prevention and control of the pandemic of SARS-CoV-2 has become more important. Among these variants, the Omicron variant has higher transmissibility and immune escape ability and is the main variant causing a large number of COVID-19 breakthrough infection, thus, presenting new challenges to pandemic prevention and control. Hence, we review the biological characteristics of the Omicron variant and discuss the current status and possible mechanism of breakthrough infection caused by the Omicron variant in order to provide insights into the prevention and control of the pandemic of SARS-CoV-2.
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