A5081340500- COVID-19 epidemiological studies
- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- Influenza Virus Research Studies
- Respiratory viral infections research
- COVID-19 Clinical Research Studies
- Animal Disease Management and Epidemiology
- Data-Driven Disease Surveillance
- Virology and Viral Diseases
- COVID-19 Pandemic Impacts
- Viral Infections and Outbreaks Research
- Virus-based gene therapy research
- Assisted Reproductive Technology and Twin Pregnancy
- Viral Infections and Vectors
- vaccines and immunoinformatics approaches
- COVID-19 and Mental Health
- Mosquito-borne diseases and control
- COVID-19 and healthcare impacts
- Parvovirus B19 Infection Studies
- COVID-19 diagnosis using AI
- Immune Response and Inflammation
- Evolution and Genetic Dynamics
- COVID-19 impact on air quality
- Animal Virus Infections Studies
- Infection Control and Ventilation
University of Oxford
2023-2025
Open Data Institute
2023-2025
Imperial College London
2018-2024
Center for Disease Dynamics, Economics & Policy
2020-2023
Science Oxford
2023
Harvard University
2020-2022
Boston University
2020
Université Paris-Sud
2020
London Centre for Neglected Tropical Disease Research
2018
Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged late 2020 despite previously high levels infection. Genome sequencing viruses sampled Manaus between November and January 2021 revealed the emergence circulation a novel SARS-CoV-2 variant concern. Lineage P.1 acquired 17 mutations, including trio spike protein (K417T, E484K, N501Y) associated with increased binding to human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular...
The COVID-19 pandemic has created a public health crisis. Because SARS-CoV-2 can spread from individuals with presymptomatic, symptomatic, and asymptomatic infections, the reopening of societies control virus will be facilitated by robust population screening, for which testing often central. After infection, undergo period incubation during viral titers are too low to detect, followed exponential growth, leading peak load infectiousness ending declining clearance. Given pattern kinetics, we...
Estimation of the effective reproductive number Rt is important for detecting changes in disease transmission over time. During Coronavirus Disease 2019 (COVID-19) pandemic, policy makers and public health officials are using to assess effectiveness interventions inform policy. However, estimation from available data presents several challenges, with critical implications interpretation course pandemic. The purpose this document summarize these illustrate them examples synthetic data, and,...
Abstract The COVID-19 pandemic has created a public health crisis. Because SARS-CoV-2 can spread from individuals with pre-symptomatic, symptomatic, and asymptomatic infections, the re-opening of societies control virus will be facilitated by robust surveillance, for which testing often central. After infection, undergo period incubation during viral titers are usually too low to detect, followed an exponential growth, leading peak load infectiousness, ending declining levels clearance....
Estimating an epidemic's trajectory is crucial for developing public health responses to infectious diseases, but case data used such estimation are confounded by variable testing practices. We show that the population distribution of viral loads observed under random or symptom-based surveillance-in form cycle threshold (Ct) values obtained from reverse transcription quantitative polymerase chain reaction testing-changes during epidemic. Thus, Ct even limited numbers samples can provide...
Abstract Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged late 2020, despite high levels previous there. Through genome sequencing viruses sampled Manaus between November 2020 and January 2021, we identified the emergence circulation a novel variant concern, lineage P.1, that acquired 17 mutations, including trio spike protein (K417T, E484K N501Y) associated with increased binding to human ACE2 receptor. Molecular clock analysis shows P.1 occurred around early was preceded by period...
The combined impact of immunity and SARS-CoV-2 variants on viral kinetics during infections has been unclear.
Abstract Background The combined impact of immunity and SARS-CoV-2 variants on viral kinetics during infections has been unclear. Methods We characterized 2,875 from the National Basketball Association occupational health cohort identified between June 2020 January 2022 using serial RT-qPCR testing. Logistic regression semi-mechanistic RNA models were used to quantify effect variant, symptom status, age, infection history, vaccination antibody titer founder strain duration potential...
Serologic studies are crucial for clarifying dynamics of the coronavirus disease pandemic. Past work on serologic (e.g., during influenza pandemics) has made relevant contributions, but specific conditions current situation require adaptation. Although detection antibodies to measure exposure, immunity, or both seems straightforward conceptually, numerous challenges exist in terms sample collection, what presence actually means, and appropriate analysis interpretation account test accuracy...
Abstract Estimation of the effective reproductive number, R t , is important for detecting changes in disease transmission over time. During COVID-19 pandemic, policymakers and public health officials are using to assess effectiveness interventions inform policy. However, estimation from available data presents several challenges, with critical implications interpretation course pandemic. The purpose this document summarize these illustrate them examples synthetic data, and, where possible,...
<h3>Importance</h3> Nursing homes and other long-term care facilities have been disproportionately impacted by the COVID-19 pandemic. Strategies are urgently needed to reduce transmission in these high-risk populations. <h3>Objective</h3> To evaluate nursing associated with contact-targeted interventions testing. <h3>Design, Setting, Participants</h3> This decision analytical modeling study developed an agent-based susceptible–exposed–infectious (asymptomatic/symptomatic)–recovered model...
Virological testing is central to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) containment, but many settings face limitations on testing. Group offers a way increase throughput by pools of combined samples; however, most proposed designs have not yet addressed key concerns over sensitivity loss and implementation feasibility. Here, we mathematical model epidemic spread empirically derived viral kinetics for SARS-CoV-2 infections identify pooling that are robust changes in...
Abstract Early in the COVID-19 pandemic, predictions of international outbreaks were largely based on imported cases from Wuhan, China, potentially missing imports other cities. We provide a method, combining daily prevalence and flight passenger volume, to estimate importations 18 Chinese cities 43 destinations, including 26 Africa. Global case China early January came primarily but inferred source shifted mid-February, especially for African destinations. that 10.4 (6.2 – 27.1) these which...
Abstract The impact of a prior SARS-CoV-2 infection on the progression subsequent infections has been unclear. Using convenience sample 94,812 longitudinal RT-qPCR measurements from anterior nares and oropharyngeal swabs, we identified 71 individuals with two well-sampled between March 11 th , 2020, July 28 2022. We compared viral kinetics first vs . second in this group, adjusting for variant, vaccination status, age. Relative to infections, usually featured faster clearance time....
Abstract Estimating an epidemic’s trajectory is crucial for developing public health responses to infectious diseases, but incidence data used such estimation are confounded by variable testing practices. We show instead that the population distribution of viral loads observed under random or symptom-based surveillance, in form cycle threshold (Ct) values, changes during epidemic and Ct values from even limited numbers samples can provide improved estimates trajectory. Combining multiple...
Estimating the durability of immunity from vaccination is complicated by unreported re-vaccination, and unobserved natural infection or reexposure, which could result in overestimation protection longevity. We tested serial cross-sectional serum samples 2005 to 2015 (N=2,530) for IgG examine measles seroprevalence, spatiotemporal patterns titers across regions antibody dynamics among children aged 1-9 years who grew up during varying circulation Madagascar under a one-dose schedule. found...
ABSTRACT Understanding acute infectious disease dynamics at individual and population levels is critical for informing public health preparedness response. Serological assays, which measure a range of biomarkers relating to humoral immunity, can provide valuable window into immune responses generated by past infections vaccinations. However, traditional methods interpreting serological data, such as binary seropositivity seroconversion thresholds, often rely on heuristics that fail account...
The rebound of endemic respiratory viruses following the COVID-19 pandemic was marked by atypical transmission dynamics, with children experiencing increased disease burden and out-of-season epidemics as restrictions relaxed. Here we used serology from a newly developed quantitative multiplex assay to assess post-pandemic immunity debt, drop in due lack virus circulation during COVID-19. We assessed age-specific antibody dynamics Seattle, Washington, US, across broad range viruses, including...
Two strains of herpes simplex virus (17, a typical type 1 strain, and HSG 52, 2 strain) are used in our Institute Glasgow for the detailed study genetics biochemistry this large DNA virus. Each strain was initially purified by repeated single-plaque isolation, cloned then isolating mutants described paper.
We present a flexible, open source R package designed to obtain biological and epidemiological insights from serological datasets. Characterising past exposures for multi-strain pathogens poses specific statistical challenge: observed antibody responses measured in assays depend on multiple unobserved prior infections that produce cross-reactive responses. provide general modelling framework jointly infer infection histories describe immune generated by these using titres against current...
serosim is an open-source R package designed to aid inference from serological studies, by simulating data arising user-specified vaccine and antibody kinetics processes using a random effects model. Serological are used assess population immunity directly measuring individuals' titers. They uncover locations and/or populations which susceptible provide evidence of past infection or vaccination help inform public health measures surveillance. Both new analytical techniques interpret them...