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Kinetics of SARS-CoV-2 infection in the human upper and lower respiratory tracts and their relationship with infectiousness

https://doi.org/10.1101/2020.09.25.20201772
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Timing of Antiviral Treatment Initiation is Critical to Reduce SARS‐CoV‐2 Viral Load
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Coronaviruses: An Overview of Their Replication and Pathogenesis
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The rate of viral transfer between upper and lower respiratory tracts determines RSV illness duration
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Clinical and biochemical indexes from 2019-nCoV infected patients linked to viral loads and lung injury
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A Systematic Review of the Clinical Utility of Cycle Threshold Values in the Context of COVID-19
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SARS-CoV-2 Viral Load Predicts Mortality in Patients with and without Cancer Who Are Hospitalized with COVID-19
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SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor
inferredcites →https://doi.org/10.1016/j.cell.2020.04.026openalex-snapshot
Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19
inferredcites →https://doi.org/10.1016/j.cell.2020.05.042openalex-snapshot
SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract
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SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant
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Pediatric Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Clinical Presentation, Infectivity, and Immune Responses
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Estimating the reproductive number R0 of SARS-CoV-2 in the United States and eight European countries and implications for vaccination
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Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series
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SARS-CoV-2 viral load predicts COVID-19 mortality
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Ebola viral dynamics in nonhuman primates provides insights into virus immuno-pathogenesis and antiviral strategies
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Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2
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SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients
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A Novel Coronavirus from Patients with Pneumonia in China, 2019
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Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility
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inferredcites →https://doi.org/10.1084/jem.20201241openalex-snapshot
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inferredcites →https://doi.org/10.1093/cid/ciaa638openalex-snapshot
Predicting Infectious Severe Acute Respiratory Syndrome Coronavirus 2 From Diagnostic Samples
inferredcites →https://doi.org/10.1098/rstb.2014.0302openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.abb2507openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.abb7314openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.abc6027openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.abc9004openalex-snapshot
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inferredcites →https://doi.org/10.1126/sciimmunol.abd1554openalex-snapshot
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inferredcites →https://doi.org/10.1126/sciimmunol.abd2071openalex-snapshot
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inferredcites →https://doi.org/10.1128/jvi.01623-05openalex-snapshot
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inferredcites →https://doi.org/10.1136/bmj.m1443openalex-snapshot
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inferredcites →https://doi.org/10.1148/radiol.2020200370openalex-snapshot
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inferredcites →https://doi.org/10.1148/radiol.2020200843openalex-snapshot
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inferredcites →https://doi.org/10.1164/arrd.1982.125.6.740openalex-snapshot
Cell number and cell characteristics of the normal human lung.
inferredcites →https://doi.org/10.1172/jci68782openalex-snapshot
Type 2 alveolar cells are stem cells in adult lung
inferredcites →https://doi.org/10.1371/journal.pbio.3001128openalex-snapshot
A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV, and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2
inferredcites →https://doi.org/10.1371/journal.pcbi.0030240openalex-snapshot
Neuraminidase Inhibitor Resistance in Influenza: Assessing the Danger of Its Generation and Spread
inferredcites →https://doi.org/10.1371/journal.pcbi.1002588openalex-snapshot
Modeling Within-Host Dynamics of Influenza Virus Infection Including Immune Responses
inferredcites →https://doi.org/10.1371/journal.pcbi.1008752openalex-snapshot
Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action
inferredcites →https://doi.org/10.2307/3802723openalex-snapshot
Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach
inferredcites →https://doi.org/10.3109/03014460.2013.807878openalex-snapshot
An estimation of the number of cells in the human body
inferredcites →https://doi.org/10.3201/eid2607.200282openalex-snapshot
High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2
inferredcites →https://doi.org/10.3201/eid2608.201142openalex-snapshot
Secondary Transmission of Coronavirus Disease from Presymptomatic Persons, China
inferredcites →https://doi.org/10.3389/fmicb.2018.01546openalex-snapshot
Mathematical Analysis of Viral Replication Dynamics and Antiviral Treatment Strategies: From Basic Models to Age-Based Multi-Scale Modeling
inferredcites →https://doi.org/10.3390/v10110627openalex-snapshot
Causes and Consequences of Spatial Within-Host Viral Spread
inferredcites →https://doi.org/10.7326/m20-2671openalex-snapshot
Contact Settings and Risk for Transmission in 3410 Close Contacts of Patients With COVID-19 in Guangzhou, China
inferredcites →https://doi.org/10.7326/m20-3012openalex-snapshot
Prevalence of Asymptomatic SARS-CoV-2 Infection
inferredcites →https://doi.org/10.7554/elife.68864openalex-snapshot
Dynamically linking influenza virus infection kinetics, lung injury, inflammation, and disease severity

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Community Transmission and Viral Load Kinetics of SARS-CoV-2 Delta (B.1.617.2)Variant in Vaccinated and Unvaccinated Individuals
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Mechanistic Modeling of SARS‐CoV‐2 and Other Infectious Diseases and the Effects of Therapeutics
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Identification of a therapeutic interfering particle—A single-dose SARS-CoV-2 antiviral intervention with a high barrier to resistance
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In silico identification of viral loads in cough-generated droplets – Seamless integrated analysis of CFPD-HCD-EWF
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Challenges in modeling the emergence of novel pathogens
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Optimizing COVID-19 control with asymptomatic surveillance testing in a university environment
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How time-scale differences in asymptomatic and symptomatic transmission shape SARS-CoV-2 outbreak dynamics
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Modelling the dynamics of SARS-CoV-2 during the first 14 days of infection
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Simplified within-host and Dose–response Models of SARS-CoV-2
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Comparative analysis of SARS-CoV-2 quasispecies in the upper and lower respiratory tract shows an ongoing evolution in the spike cleavage site
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Making waves: Integrating wastewater surveillance with dynamic modeling to track and predict viral outbreaks
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Innate Immunity Plays a Key Role in Controlling Viral Load in COVID-19: Mechanistic Insights from a Whole-Body Infection Dynamics Model
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Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness
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A simple model of COVID-19 explains disease severity and the effect of treatments
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Modeling how antibody responses may determine the efficacy of COVID-19 vaccines
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Modeling SARS-CoV-2 viral kinetics and association with mortality in hospitalized patients from the French COVID cohort
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The total number and mass of SARS-CoV-2 virions
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Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis
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Effect of remdesivir on viral dynamics in COVID-19 hospitalized patients: a modelling analysis of the randomized, controlled, open-label DisCoVeRy trial
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Decomposing the sources of SARS-CoV-2 fitness variation in the United States
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Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections?
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The SARS-CoV-2 pandemic: remaining uncertainties in our understanding of the epidemiology and transmission dynamics of the virus, and challenges to be overcome
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Estimation of viral kinetics model parameters in young and aged SARS-CoV-2 infected macaques
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A within-host birth–death and time–dose–response model for Legionnaires’ disease
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Autocrine and paracrine interferon signalling as ‘ring vaccination’ and ‘contact tracing’ strategies to suppress virus infection in a host
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A within-host model of SARS-CoV-2 infection
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How reliable are estimates of key parameters in viral dynamic models?
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Modelling the Dynamics of SARS-CoV-2 during early phase of infection
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Using in silico viral kinetic models to guide therapeutic strategies during a pandemic: An example in SARS‐CoV‐2
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Spatially structured models of viral dynamics: a scoping review
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Differences in virus and immune dynamics for SARS-CoV-2 Delta and Omicron infections by age and vaccination histories
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Lessons learned from modeling COVID-19 and steps to take at the start of the next pandemic focusing on ensemble models
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A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV, and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2
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Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies
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Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action
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Quantifying dose-, strain-, and tissue-specific kinetics of parainfluenza virus infection
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Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection
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Disentangling the dynamical underpinnings of differences in SARS-CoV-2 pathology using within-host ecological models
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Modeling recapitulates the heterogeneous outcomes of SARS-CoV-2 infection and quantifies the differences in the innate immune and CD8 T-cell responses between patients experiencing mild and severe symptoms
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Differences in virus and immune dynamics for SARS-CoV-2 Delta and Omicron infections by age and vaccination histories
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Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility
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Mathematical Modeling of Remdesivir to Treat COVID-19: Can Dosing Be Optimized?
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Quantification of the Tradeoff between Test Sensitivity and Test Frequency in a COVID-19 Epidemic—A Multi-Scale Modeling Approach
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Modeling the Influence of Vaccine Administration on COVID-19 Testing Strategies
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Harnessing the Capability of CADD Methods in the Prediction of Anti-COVID Drug Likeliness
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Joint mechanistic modeling of viral and antibody responses to vaccines in non-human primates to quantify SARS-CoV-2 mechanistic correlates of protection
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Quantifying the relationship between SARS-CoV-2 viral load and infectiousness
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Inference of the SARS-CoV-2 generation time using UK household data
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Modelling the response to vaccine in non-human primates to define SARS-CoV-2 mechanistic correlates of protection
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