Estimation of age-stratified contact rates during the COVID-19 pandemic using a novel inference algorithm

Well parameterised epidemiological models including accurate representation of contacts, are fundamental to controlling epidemics. However, age-stratified contacts are typically estimated from pre-pandemic/peace-time surveys, even though interventions and public response likely alter contacts. Here we fit age-stratified models, including re-estimation of relative contact rates between age-classes, to public data describing the 2020-21 COVID-19 outbreak in England. This data includes age-stratified population size, cases, deaths, hospital admissions, and results from the Coronavirus Infection Survey (almost 9000 observations in all). Fitting stochastic compartmental models to such detailed data is extremely challenging, especially considering the large number of model parameters being estimated (over 150). An efficient new inference algorithm ABC-MBP combining existing Approximate Bayesian Computation (ABC) methodology with model-based proposals (MBP) is applied. Modified contact rates are inferred alongside time-varying reproduction numbers that quantify changes in overall transmission due to pandemic response, and age-stratified proportions of asymptomatic cases, hospitalisation rates and deaths. These inferences are robust to a range of assumptions including the values of parameters that cannot be estimated from available data. ABC-MBP is shown to enable reliable joint analysis of complex epidemiological data yielding consistent parametrisation of dynamic transmission models that can inform data-driven public health policy and interventions.

First National Genomic Epidemiological Study of Neisseria gonorrhoeae Strains Spreading Across Sweden in 2016

The increasing transmission and antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global health concern with worrying trends of decreasing susceptibility to also the last-line extended-spectrum cephalosporin (ESC) ceftriaxone. A dramatic increase of reported gonorrhea cases has been observed in Sweden from 2016 and onward. The aim of the present study was to comprehensively investigate the genomic epidemiology of all cultured N. gonorrhoeae isolates in Sweden during 2016, in conjunction with phenotypic AMR and clinical and epidemiological data of patients. In total, 1279 isolates were examined. Etest and whole-genome sequencing (WGS) were performed, and epidemiological data obtained from the Public Health Agency of Sweden. Overall, 51.1%, 1.7%, and 1.3% resistance to ciprofloxacin, cefixime, and azithromycin, respectively, was found. No isolates were resistant to ceftriaxone, however, 9.3% of isolates showed a decreased susceptibility to ceftriaxone and 10.5% to cefixime. In total, 44 penA alleles were found of which six were mosaic (n = 92). Using the typing schemes of MLST, NG-MAST, and NG-STAR; 133, 422, and 280 sequence types, respectively, and 93 NG-STAR clonal complexes were found. The phylogenomic analysis revealed two main lineages (A and B) with lineage A divided into two main sublineages (A1 and A2). Resistance and decreased susceptibility to ESCs and azithromycin and associated AMR determinants, such as mosaic penA and mosaic mtrD, were predominantly found in sublineage A2. Resistance to cefixime and azithromycin was more prevalent among heterosexuals and MSM, respectively, and both were predominantly spread through domestic transmission. Continuous surveillance of the spread and evolution of N. gonorrhoeae, including phenotypic AMR testing and WGS, is essential for enhanced knowledge regarding the dynamic evolution of N. gonorrhoeae and gonorrhea epidemiology.

Dynamics and optimal control of a spatial diffusion HIV/AIDS model with ART and PrEP treatments

In this paper, to investigate the synthetic effect of PrEP (pre-exposure prophylaxis) and ART (antiretrovial therapy) on HIV transmission among MSM (men who have sex with men) in heterogenous environment, an realistic HIV epidemic model with spatial diffusion is established. Here, HIV infectious people are divided into three immunity based compartments, i.e., CD4+ T cell count less than 350, between 350 and 500, and more than 500, respectively. The basic reproduction number $R_0$ is established and proved as a threshold parameter: The global asymptotic stability of the disease-free steady state holds for $R_0<1$, and the disease will be present if $R_0>1$. Considering the substantial advantages of PrEP and ART in controlling HIV transmissions among MSM, the optimal control problem is presented for the case of positive constant diffusion coefficients, which minimize the total population of susceptible individual and HIV infected individual, the cost of PrEP and ART thearpy. As an illustration of our theoretical results, we conduct numerical simulations. We also conduct an optimal control case study where model parameters are estimated from the demographic and epidemiological data from China. This work suggests: (1) Spatial factors cannot be ignored during the HIV intervention; (2)Taking the PrEP intervention measure for HIV transmissions among MSM as early as possible will help to improve the control efficiency and reduces its cost; (3) Reducing the PrEP drug costs will promote the efficiency of PrEP treatment in preventing the spread of HIV among MSM.

The global epidemiology of chikungunya from 1999 to 2020: A systematic literature review to inform the development and introduction of vaccines

Chikungunya fever is an acute febrile illness that is often associated with severe polyarthralgia in humans. The disease is caused by chikungunya virus (CHIKV), a mosquito-borne alphavirus. Since its reemergence in 2004, the virus has spread throughout the tropical world and several subtropical areas affecting millions of people to become a global public health issue. Given the significant disease burden, there is a need for medical countermeasures and several vaccine candidates are in clinical development. To characterize the global epidemiology of chikungunya and inform vaccine development, we undertook a systematic literature review in MEDLINE and additional public domain sources published up to June 13, 2020 and assessed epidemiological trends from 1999 to 2020. Observational studies addressing CHIKV epidemiology were included and studies not reporting primary data were excluded. Only descriptive analyses were conducted. Of 3,883 relevant sources identified, 371 were eligible for inclusion. 46% of the included studies were published after 2016. Ninety-seven outbreak reports from 45 countries and 50 seroprevalence studies from 31 countries were retrieved, including from Africa, Asia, Oceania, the Americas, and Europe. Several countries reported multiple outbreaks, but these were sporadic and unpredictable. Substantial gaps in epidemiological knowledge were identified, specifically granular data on disease incidence and age-specific infection rates. The retrieved studies revealed a diversity of methodologies and study designs, reflecting a lack of standardized procedures used to characterize this disease. Nevertheless, available epidemiological data emphasized the challenges to conduct vaccine efficacy trials due to disease unpredictability. A better understanding of chikungunya disease dynamics with appropriate granularity and better insights into the duration of long-term population immunity is critical to assist in the planning and success of vaccine development efforts pre and post licensure.

Implementing coronavirus disease 2019 scale-up registry protocol in national multiple sclerosis registry system of Iran

Background: The national multiple sclerosis (MS) registry is aimed at monitoring and improving quality of care and providing feedback to improve health outcomes by systematic recording of data. In 2018, the nationwide MS registry of Iran (NMSRI) was initiated for collecting epidemiological data and information on health care provision for patients with MS. The aim of the current study was to introduce the role of implementing coronavirus disease 2019 (COVID-19) scale-up registry protocol in NMSRI and arrange the national MS generality with information obtained during the COVID-19 pandemic. Methods: The NMSRI group set up a program with crucial elements to collect the data of patients with MS who developed COVID-19. All MS cases with confirmed diagnosis of COVID-19 were enrolled in this study. New elements were considered to be added into the dataset, including demographic characteristics, definite diagnosis of COVID-19 and its symptoms, history of comorbidities, history of medications and hospitalization, changes in magnetic resonance imaging (MRI), and infection outcomes. Results: The COVID-19 data collection program was designed in NMSRI to collect data of MS cases with COVID-19 infection. The data collection protocol was explained to neurologists through an online training workshop. To the date of the study, 21 centers from 17 provinces of Iran were involved in the COVID-19 databases promoting NMSRI and 612 participants were registered successfully. Conclusion: We extended an agreement on data collection and developed it in NMSRI with various contributors to discover a critical need for COVID-19 awareness and monitor clinical training in MS.

Remdesivir and dexamethasone as tools to relieve hospital care systems stressed by COVID-19: A modelling study on bed resources and budget impact

Remdesivir and dexamethasone are the only drugs providing reductions in the lengths of hospital stays for COVID-19 patients. We assessed the impacts of remdesivir on hospital-bed resources and budgets affected by the COVID-19 outbreak. A stochastic agent-based model was combined with epidemiological data available on the COVID-19 outbreak in France and data from two randomized control trials. Strategies involving treating with remdesivir only patients with low-flow oxygen and patients with low-flow and high-flow oxygen were examined. Treating all eligible low-flow oxygen patients during the entirety of the second wave would have decreased hospital-bed occupancy in conventional wards by 4% [2%; 7%] and intensive care unit (ICU)-bed occupancy by 9% [6%; 13%]. Extending remdesivir use to high-flow-oxygen patients would have amplified reductions in ICU-bed occupancy by up to 14% [18%; 11%]. A minimum remdesivir uptake of 20% was required to observe decreases in bed occupancy. Dexamethasone had effects of similar amplitude. Depending on the treatment strategy, using remdesivir would, in most cases, generate savings (up to 722€) or at least be cost neutral (an extra cost of 34€). Treating eligible patients could significantly limit the saturation of hospital capacities, particularly in ICUs. The generated savings would exceed the costs of medications.

A Coupled Experimental and Statistical Approach for an Assessment of the Airborne Infection Risk in Event Locations

Operators of event locations are particularly affected by a pandemic. Resulting restrictions may cause uneconomical business. With previous models, only an incomplete quantitative risk assessments is possible, whereby no suitable restrictions can be derived. Hence, a mathematical and statistical model has been developed in order to link measurement data of substance dispersion in rooms with epidemiological data like incidences, reproduction numbers, vaccination rates and test qualities. This allows a first time overall assessment of airborne infection risks in large event locations. In these venues displacement ventilation concepts are often implemented. In this case simplified theoretical assumptions fail for the prediction of relevant airflows for infection processes. Thus, with locally resolving trace gas measurements and specific data of infection processes, individual risks can be computed more detailed. Via inclusion of many measurement positions, an assessment of entire event locations is possible. Embedding the overall model in a flexible application, daily updated epidemiological data allow latest calculations of expected new infections and individual risks of single visitors for a certain event. With this model, an instrument has been created that can help policymakers and operators to take appropriate measures and to check restrictions for their effect.

The Global Spread of Severe Obesity in Toddlers, Children and Adolescents – a Systematic Review & Meta Analysis

Introduction: Severe obesity among children and adolescents has emerged as a public health concern in multiple places around the world. Methods: We searched the Medline database for articles on severe obesity rates in children published between January 1960 and January 2020. For studies with available prevalence rates for an early and a more recent time period, the relative increase in prevalence was imputed. Results: In total, 874 publications were identified, of which 38 contained relevant epidemiological data. Rates of severe obesity varied significantly according to age, gender, geographic area, and the definition of severe obesity. The highest rates of class II and III obesity in the US according to the Centers of Disease Control cutoff were 9.5% and 4.5%, respectively. Seventeen studies reported prevalence rates in at least two time periods. Data for 9,190,718 individuals showed a 1.71 (95%CI, 1.53-1.90) greater odds for severe obesity in 2006-2017 (N=5,029,584) vs. 1967-2007 (N=4,161,134). In an analysis limited to studies from 1980s’ with a minimum follow-up of 20 years, a 9.16(95%CI, 7.76-10.80) greater odds for severe obesity in recent vs. earlier time was found. An analysis limited to studies from 2000, with a follow-up of 5-15 years, a 1.09 (95%CI, 0.99-1.20) greater odds was noted when comparing (2011-2017; N=4,991,831) vs. (2000-2011; N=4,134,340). Conclusion: Severe pediatric obesity is escalating with a marked increase from the1980’s and a slower rate from 2000.

Treatment of Human Sporotrichosis Caused by Sporothrix brasiliensis

We describe the successful treatment of a series of 30 zoonotic sporotrichosis cases from southern Brazil. Sporothrix brasiliensis was the species genotypically identified in all 25 confirmed cases. Five other cases were classified as probable, without laboratory confirmation, but with clinical and epidemiological data of cat-transmitted sporotrichosis. Two isolates were sequenced by translation elongation factor-1 alpha (EF1α) loci in order to compare their sequences, and both of them showed distinct genotypes from S. brasiliensis strains from other Brazilian states. Itraconazole (ITZ) or potassium iodide (KI) were the first choice treatment in 28 and 2 cases, respectively. Microdilution assay showed a wild-type profile of S. brasiliensis isolates to ITZ. However, a lack of clinical response occurred in 42% of cases, especially those treated with ITZ 100 mg/day, and treatment needed modifications, by either increased doses or antifungal combinations. Clinical cure required a mean of 187 days of treatment, which was dependent on the clinical form of the disease and age of patients. Therapy, including dosages and durations, for cutaneous forms of sporotrichosis requires re-evaluation, since cases caused by S. brasiliensis may influence treatment efficacy.

Scabies epidemiology in health care centers for refugees and asylum seekers in Greece

Background Scabies is a global health concern disproportionally affecting vulnerable population such as refugees and asylum seekers. Greece is a main geographical point of entry in Europe for refugees, but epidemiological data on scabies in this population is scarce. We aimed to evaluate the epidemiology of scabies, including trends over the study period. Methodology/Principal findings Data were collected from June, 2016 to July, 2020, using the surveillance system of the Greek National Public Health Organization. Staff at health centers for refugees/asylum seekers compiled daily reports on scabies and other infectious diseases. Observed proportional morbidity for scabies was calculated using consultations for scabies as a proportion of total consultations. There were a total of 13118 scabies cases over the study period. Scabies was the third most frequently observed infectious disease in refugees/asylum seekers population after respiratory infections and gastroenteritis without blood in the stool. The scabies monthly observed proportional morbidity varied between 0.3% (August 2017) to 5.6% (January 2020). Several outbreaks were documented during the study period. An increasing number of cases was observed from October 2019 until the end of the study period, with a peak of 1663 cases in January 2020, related to an outbreak at one center. Spearman correlation test between the number of reported scabies cases and time confirmed an increasing trend (ρ=0.67). Conclusions/Significance Scabies is one of the most frequently reported infectious diseases by health care workers in refugee/asylum seekers centers in Greece. Consultations for scabies increased over time and there were several outbreaks. The current surveillance system effectively detects new cases in an early stage. Public health interventions, including mass drug administration, should be considered to reduce the burden of scabies in refugee/migrant populations.