Katherine E. Atkins
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View article: Continuing to be cautious: Japanese contact patterns during the COVID-19 pandemic and their association with public health recommendations
Continuing to be cautious: Japanese contact patterns during the COVID-19 pandemic and their association with public health recommendations Open
Despite implementing no lockdowns and having a large elderly population, Japan had a low mortality rate due to COVID-19 compared to Europe and North America. The extent to which policies impacted person-to-person contact remains unclear. I…
View article: Multiple mechanisms of strain competition are needed to explain pneumococcal serotype-specific antibiotic resistance patterns
Multiple mechanisms of strain competition are needed to explain pneumococcal serotype-specific antibiotic resistance patterns Open
2 Abstract Background Disease caused by antibiotic resistant pneumococcal strains is an important public health concern. The impact of public health interventions depend on the complex ecology governing serotype and antibiotic resistant st…
View article: Continuing to be Cautious: Japanese Contact Patterns during the COVID-19 Pandemic and their Association with Public Health Recommendations
Continuing to be Cautious: Japanese Contact Patterns during the COVID-19 Pandemic and their Association with Public Health Recommendations Open
Despite implementing no lockdowns and having a large elderly population, Japan had a low mortality rate due to COVID-19 compared to Europe and North America. The extent to which policies impacted person-to-person contact remains unclear. I…
View article: Estimating the risk and spatial spread of measles in populations with high MMR uptake: Using school-household networks to understand the 2013 to 2014 outbreak in the Netherlands
Estimating the risk and spatial spread of measles in populations with high MMR uptake: Using school-household networks to understand the 2013 to 2014 outbreak in the Netherlands Open
Background Measles outbreaks are still routine, even in countries where vaccination coverage exceeds the guideline of 95%. Therefore, achieving ambitions for measles eradication will require understanding of how unvaccinated children inter…
View article: Reconciling founder variant multiplicity of HIV-1 infection with the rate of CD4 <sup>+</sup> decline
Reconciling founder variant multiplicity of HIV-1 infection with the rate of CD4 <sup>+</sup> decline Open
HIV-1 transmission precipitates a stringent genetic bottleneck, with 75% of new infections initiated by a single genetic variant. Where multiple variants initiate infection, recipient set point viral load (SpVL) and the rate of CD4 + T cel…
View article: Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity
Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity Open
A standard method in phylogenetic reconstruction for representing variation in substitution rates between sites in the genome is the discrete Gamma model (DGM). Relative rates are assumed to be distributed according to a discretised Gamma …
View article: Reconciling founder variant multiplicity of HIV-1 infection with the rate of CD4<sup>+</sup>decline
Reconciling founder variant multiplicity of HIV-1 infection with the rate of CD4<sup>+</sup>decline Open
Three quarters of new HIV-1 infections are reported to be initiated by a single genetic variant. Infections initiated by multiple variants have been linked with higher recipient set point viral loads (SpVL) and a faster rate of CD4 + T cel…
View article: Anticipating the risk and spatial spread of measles in populations with high MMR uptake: using school-household networks to understand the 2013 - 2014 outbreak in the Netherlands
Anticipating the risk and spatial spread of measles in populations with high MMR uptake: using school-household networks to understand the 2013 - 2014 outbreak in the Netherlands Open
Measles outbreaks are still routine, even in countries where vaccination coverage exceeds the guideline of 95%. Therefore, achieving ambitions for measles eradication will require understanding how unvaccinated children interact with other…
View article: Protecting infants against RSV disease: an impact and cost-effectiveness comparison of long-acting monoclonal antibodies and maternal vaccination
Protecting infants against RSV disease: an impact and cost-effectiveness comparison of long-acting monoclonal antibodies and maternal vaccination Open
National Institute for Health Research.
View article: Vaccination of Older Adults Against Respiratory Syncytial Virus: The Final Pieces of the Puzzle
Vaccination of Older Adults Against Respiratory Syncytial Virus: The Final Pieces of the Puzzle Open
With an estimated 186,000-614,000 older adults hospitalised annually as a result of respiratory syncytial virus (RSV) infection and with no effective treatment, there is an unmet need to prevent these infections, many of which lead to deat…
View article: Inferring the multiplicity of founder variants initiating HIV-1 infection: a systematic review and individual patient data meta-analysis
Inferring the multiplicity of founder variants initiating HIV-1 infection: a systematic review and individual patient data meta-analysis Open
Medical Research Council Precision Medicine Doctoral Training Programme and a European Research Council Starting Grant.
View article: Evaluating the impact of Respiratory Syncytial Virus immunisation strategies on antibiotic use and drug resistant bacterial infections in England
Evaluating the impact of Respiratory Syncytial Virus immunisation strategies on antibiotic use and drug resistant bacterial infections in England Open
Background: Vaccines against viruses have been proposed as a novel means to reduce antibiotic use, which would, in turn, decrease selection for antibiotic resistant bacteria. However, the impact of this intervention is poorly quantified, a…
View article: Optimal Respiratory Syncytial Virus intervention programmes using Nirsevimab in England and Wales
Optimal Respiratory Syncytial Virus intervention programmes using Nirsevimab in England and Wales Open
Nirsevimab has the potential to be cost-effective in England and Wales not only for use in high-risk infants.
View article: Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs
Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs Open
Inferring the transmission direction between linked individuals living with HIV provides unparalleled power to understand the epidemiology that determines transmission. Phylogenetic ancestral-state reconstruction approaches infer the trans…
View article: Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools
Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools Open
The global spread of coronavirus disease 2019 (COVID-19) has emphasized the need for evidence-based strategies for the safe operation of schools during pandemics that balance infection risk with the society’s responsibility of allowing chi…
View article: Optimal Respiratory Syncytial Virus intervention programmes using Nirsevimab in England and Wales
Optimal Respiratory Syncytial Virus intervention programmes using Nirsevimab in England and Wales Open
Introduction Respiratory Syncytial Virus (RSV) is a major cause of acute lower respiratory tract infections (ALRI) in infants. There are no licensed vaccines and only one monoclonal antibody available to protect infants from disease. A new…
View article: akira-endo/schooldynamics_FluMatsumoto14-15: Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools
akira-endo/schooldynamics_FluMatsumoto14-15: Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools Open
Incorporated changes associated with the revised version of Endo et al. "Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools"
View article: Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa
Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa Open
The Sustainable East Africa Research in Community Health (SEARCH) trial was a universal test-and-treat (UTT) trial in rural Uganda and Kenya, aiming to lower regional HIV-1 incidence. Here, we quantify breakthrough HIV-1 transmissions occu…
View article: Genomic epidemiology of circulating SARS-CoV-2 variants during first two years of the pandemic in Colombia
Genomic epidemiology of circulating SARS-CoV-2 variants during first two years of the pandemic in Colombia Open
The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for mo…
View article: Genomic epidemiology of circulating SARS-CoV-2 variants during first two years of the pandemic in Colombia
Genomic epidemiology of circulating SARS-CoV-2 variants during first two years of the pandemic in Colombia Open
The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for mo…
View article: SCoVMod – a spatially explicit mobility and deprivation adjusted model of first wave COVID-19 transmission dynamics
SCoVMod – a spatially explicit mobility and deprivation adjusted model of first wave COVID-19 transmission dynamics Open
Background : Mobility restrictions prevent the spread of infections to disease-free areas, and early in the coronavirus disease 2019 (COVID-19) pandemic, most countries imposed severe restrictions on mobility as soon as it was clear that …
View article: The local burden of disease during the first wave of the COVID-19 epidemic in England: estimation using different data sources from changing surveillance practices
The local burden of disease during the first wave of the COVID-19 epidemic in England: estimation using different data sources from changing surveillance practices Open
Background The COVID-19 epidemic has differentially impacted communities across England, with regional variation in rates of confirmed cases, hospitalisations and deaths. Measurement of this burden changed substantially over the first mont…