Publications by authors named "Katherine E Atkins"

Article Synopsis
  • HIV-1 transmission typically starts with a single genetic variant in 75% of new infections, leading to a genetic bottleneck.
  • Studies on multiple variant infections suggest they might elevate viral load and speed up CD4 T cell decline, but results have been inconsistent.
  • Our analysis shows many studies lacked the statistical power to confirm these effects, and our models indicate that a faster CD4 decline isn't automatically linked to multiple variant infections without a clear cause-and-effect relationship.
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  • Measles outbreaks persist even in areas with high vaccination rates, revealing the need to study interactions among unvaccinated children, particularly in school and home settings in the Netherlands, where outbreaks have occurred since the introduction of the MMR vaccine.
  • Researchers created a contact network among primary and secondary schools based on household pairs to assess the risk of measles spread, emphasizing that schools with low vaccine uptake are highly interconnected.
  • Their network-based model accurately simulated a significant measles outbreak in 2013, showing a much better alignment with real data compared to alternative models that ignored network dynamics and vaccine data.
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Background: Two new products for preventing Respiratory Syncytial Virus (RSV) in young children have been licensed: a single-dose long-acting monoclonal antibody (la-mAB) and a maternal vaccine (MV). To facilitate the selection of new RSV intervention programmes for large-scale implementation, this study provides an assessment to compare the costs of potential programmes with the health benefits accrued.

Methods: Using an existing dynamic transmission model, we compared maternal vaccination to la-mAB therapy against RSV in England and Wales by calculating the impact and cost-effectiveness.

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Article Synopsis
  • * Researchers analyzed over 14,000 complete SARS-CoV-2 genomes using Bayesian phylodynamic methods to estimate key epidemiological metrics, including when variants were introduced and how effective control measures were.
  • * The findings reveal 188 circulating Pango lineages in Colombia, with significant fluctuations in transmission rates, underscoring the importance of genomic surveillance for guiding public health interventions against emerging variants.
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Background: HIV-1 infections initiated by multiple founder variants are characterised by a higher viral load and a worse clinical prognosis than those initiated with single founder variants, yet little is known about the routes of exposure through which transmission of multiple founder variants is most probable. Here we used individual patient data to calculate the probability of multiple founders stratified by route of HIV exposure and study methodology.

Methods: We conducted a systematic review and meta-analysis of studies that estimated founder variant multiplicity in HIV-1 infection, searching MEDLINE, Embase, and Global Health databases for papers published between Jan 1, 1990, and Sept 14, 2020.

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Article Synopsis
  • - Respiratory Syncytial Virus (RSV) significantly impacts infants with acute lower respiratory tract infections, and while there’s currently only one monoclonal antibody available, a new one called Nirsevimab has shown promising results in trials.
  • - The study used a dynamic model to evaluate various Nirsevimab administration strategies, including seasonal and catch-up approaches, to determine their cost-effectiveness against the existing treatment, Palivizumab.
  • - Nirsevimab would need to be priced at £63 or less per dose to cost-effectively replace Palivizumab for seasonal administration, with an extended seasonal approach being optimal at £32/dose or less, indicating its potential value beyond just high-risk infants in
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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 transmission direction by identifying the individual in whom the most recent common ancestor of the virus populations originated. While these methods vary in accuracy, it is unclear why.

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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 children to attend school. Due to limited empirical data, existing analyses assessing school-based interventions in pandemic situations often impose strong assumptions, for example, on the relationship between class size and transmission risk, which could bias the estimated effect of interventions, such as split classes and staggered attendance. To fill this gap in school outbreak studies, we parameterized an individual-based model that accounts for heterogeneous contact rates within and between classes and grades to a multischool outbreak data of influenza.

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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 occurring during the trial from population-based, dried blood spot samples. Between 2013 and 2017, we obtained 549 and 488 HIV-1 consensus sequences from 745 participants: 469 participants infected prior to trial commencement and 276 SEARCH-incident infections.

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: 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 containment of local outbreaks was insufficient to control spread. These restrictions have adverse impacts on the economy and other aspects of human health, and it is important to quantify their impact for evaluating their future value. : Here we develop Scotland Coronavirus transmission Model (SCoVMod), a model for COVID-19 in Scotland, which presents unusual challenges because of its diverse geography and population conditions.

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Article Synopsis
  • Researchers analyzed hospital COVID-19 transmission using viral genomic and epidemiological data from 2181 patients and staff at a UK NHS Trust during two pandemic waves.
  • Findings indicated a drop in staff-to-staff transmission from 31.6% to 12.9%, while patient-to-patient transmission surged from 27.1% to 52.1%.
  • Control measures effectively curbed staff infections but failed to stop rising patient transmissions; thus, better detection of hospital-acquired cases is crucial to disrupt these transmission chains.
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  • Our study investigated the impacts of socio-economic and ethnic factors on the spread of Influenza A(H1N1)pdm09 during the 2009 pandemic in Birmingham and London, revealing significant disparities in health outcomes based on ethnicity and deprivation status.
  • We found that South Asian individuals and residents in deprived areas faced higher rates of infection, with school-aged children in the most deprived communities being 2.8 times more likely to be infected.
  • The analysis indicates that these health disparities fluctuate over time and suggest that social group clustering contributed to the outbreak's spread among different communities.
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Schools play a central role in the transmission of many respiratory infections. Heterogeneous social contact patterns associated with the social structures of schools (i.e.

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Drug resistance mutations appear in HIV under treatment pressure. Resistant variants can be transmitted to treatment-naive individuals, which can lead to rapid virological failure and can limit treatment options. Consequently, quantifying the prevalence, emergence and transmission of drug resistance is critical to effectively treating patients and to shape health policies.

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Vaccines against bacterial pathogens can protect recipients from becoming infected with potentially antibiotic-resistant pathogens. However, by altering the selective balance between antibiotic-sensitive and antibiotic-resistant bacterial strains, vaccines may also suppress-or spread-antibiotic resistance among unvaccinated individuals. Predicting the outcome of vaccination requires knowing what drives selection for drug-resistant bacterial pathogens and what maintains the circulation of both antibiotic-sensitive and antibiotic-resistant strains of bacteria.

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Background: Predicting bed occupancy for hospitalised patients with COVID-19 requires understanding of length of stay (LoS) in particular bed types. LoS can vary depending on the patient's "bed pathway" - the sequence of transfers of individual patients between bed types during a hospital stay. In this study, we characterise these pathways, and their impact on predicted hospital bed occupancy.

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Background: Respiratory syncytial virus (RSV) represents a substantial burden of disease in young infants in low-income and middle-income countries (LMICs). Because RSV passive immunisations, including maternal vaccination and monoclonal antibodies, can only grant a temporary period of protection, their effectiveness and efficiency will be determined by the timing of the immunisation relative to the underlying RSV seasonality. We aimed to assess the potential effect of different approaches for passive RSV immunisation of infants in LMICs.

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Contact tracing has the potential to control outbreaks without the need for stringent physical distancing policies, e.g. civil lockdowns.

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In early 2020 many countries closed schools to mitigate the spread of SARS-CoV-2. Since then, governments have sought to relax the closures, engendering a need to understand associated risks. Using address records, we construct a network of schools in England connected through pupils who share households.

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The current pediatric vaccination program in England and Wales administers Live-Attenuated Influenza Vaccine (LAIV) to children ages 2-16 years old. Annual administration of LAIV to this age group is costly and poses substantial logistical issues. This study aims to evaluate the cost-effectiveness of prioritizing vaccination to age groups within the 2-16 year old age range to mitigate the operational and resource challenges of the current strategy.

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Background: With a suite of promising new RSV prophylactics on the horizon, including long-acting monoclonal antibodies and new vaccines, it is likely that one or more of these will replace the current monoclonal Palivizumab programme. However, choosing the optimal intervention programme will require balancing the costs of the programmes with the health benefits accrued.

Methods: To compare the next generation of RSV prophylactics, we integrated a novel transmission model with an economic analysis.

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