Infectious Disease Epidemiology Research Articles

The impact of COVID-19 lockdown on infectious diseases epidemiology: The experience of a tertiary Italian Pediatric Emergency Department.

IntroductionThe aim of this study was to describe the rate and types of community-acquired respiratory infections observed in a pediatric ED during the SARS-CoV-2 related lockdown in Italy and to compare data with the same period of previous year.MethodsA retrospective analysis of medical charts of patients arrived at the ED of Gaslini Children's Hospital from 10th March 2020 to 30th April 2019 and the same frame of 2020 were performed. We compared two groups by demographics, duration of fever before ED admission, triage code, number of patients hospitalized after ED evaluation. We calculated proportion and incidence rate for airborne infections, fever, and urinary tract infections (UTI), appendicitis, and gastroenteritis for control.Results1362 children arrived at the ED during the lockdown compared to 5628 in the same period of 2019 (−75,8%). No difference was noticed (27.7% vs 28.4%) in the total amount of infectious episodes. A significant reduction in rate of incidence and proportion were observed for upper respiratory tract infections (21,4% vs 28%), otitis (2,6% vs 16,2%), streptococcal infections (0,5% vs 5,2%) and bronchiolitis (2,1% vs 5,7%). Conversely, FUO (27,8 vs 11,1%), infectious mononucleosis (2,6% vs 0,4%), UTI (7,4% vs 2,9%) and appendicitis (6,8% vs 1,1%) significantly increased. Median time from the onset of fever and arrival in ED was significantly lower in 2020 group.ConclusionOur results demonstrated a reduction in community-acquired respiratory infections during the lockdown for COVID-19. The increase in rate of FUO and febrile conditions, together with the short time from fever onset and ED visit could be related to the fear for a SARS-CoV-2 infection.

Sequencing the pandemic: rapid and high-throughput processing and analysis of COVID-19 clinical samples for 21st century public health

Genomic epidemiology has proven successful for real-time and retrospective monitoring of small and large-scale outbreaks. Here, we report two genomic sequencing and analysis strategies for rapid-turnaround or high-throughput processing of metagenomic samples. The rapid-turnaround method was designed to provide a quick phylogenetic snapshot of samples at the heart of active outbreaks, and has a total turnaround time of <48 hours from raw sample to analyzed data. The high-throughput method was designed for semi-retrospective data analysis, and is both cost effective and highly scalable. Though these methods were developed and utilized for the SARS-CoV-2 pandemic response in Arizona, U.S, and we envision their use for infectious disease epidemiology in the 21st Century.

Prevalence and Antimicrobial Resistance of Enteropathogenic Bacteria in Yellow-Legged Gulls (Larus michahellis) in Southern Italy.

Simple SummarySeveral Mediterranean countries have suffered from a significant increase in the populations of gulls. These birds are agile fliers and are able to adapt easily to different habitats and to profit from food discarded by humans. In addition, gulls may be considered by some as pests, given their interactions with human activities, and have been described as carriers, but actually function as environmental sentinels of enteropathogenic bacteria and antibiotic-resistant strains. Therefore, the aim of this study was to examine the role of gulls as vectors of zoonotic agents of high importance for human health and as potential reservoirs of antimicrobial-resistant strains.Wild birds may host and spread pathogens, integrating the epidemiology of infectious diseases. Particularly, Larus spp. have been described as responsible for the spread of many enteric diseases, primarily because of their large populations at landfill sites. The aim of this study was to examine the role of yellow-legged gulls as a source of enteropathogenic bacteria such as Campylobacter spp., Salmonella spp., Shiga toxin-producing Escherichia coli and Yersinia spp., with particular attention to antibiotic-resistant strains. Enteropathogenic bacteria were isolated from 93/225 yellow-legged gulls examined from April to July, during a four-year period (2016–2019). Specifically, Campylobacter spp. was isolated from 60/225 samples (26.7%), and identified as C. coli (36/60) and as C. jejuni (24/60). Salmonella spp. was isolated from 3/225 samples (1.3%), and identified as Salmonella arizonae. Shiga toxin-producing E. coli were isolated from 30/225 samples (13.3%) samples, and serotyped as E. coli O128 (12/30) O26 (9/30), O157 (6/30) and O11 (3/30); Yersinia spp. was never detected. Isolated strains exhibited multidrug resistance, including vitally important antibiotics for human medicine (i.e., fluoroquinolones, tetracyclines). Our study emphasizes the importance of yellow-legged gulls as potential reservoirs of pathogenic and resistant strains and their involvement in the dissemination of these bacteria across different environments, with resulting public health concerns.

Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019.

Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.

Inferring high-resolution human mixing patterns for disease modeling

Mathematical and computational modeling approaches are increasingly used as quantitative tools in the analysis and forecasting of infectious disease epidemics. The growing need for realism in addressing complex public health questions is, however, calling for accurate models of the human contact patterns that govern the disease transmission processes. Here we present a data-driven approach to generate effective population-level contact matrices by using highly detailed macro (census) and micro (survey) data on key socio-demographic features. We produce age-stratified contact matrices for 35 countries, including 277 sub-national administratvie regions of 8 of those countries, covering approximately 3.5 billion people and reflecting the high degree of cultural and societal diversity of the focus countries. We use the derived contact matrices to model the spread of airborne infectious diseases and show that sub-national heterogeneities in human mixing patterns have a marked impact on epidemic indicators such as the reproduction number and overall attack rate of epidemics of the same etiology. The contact patterns derived here are made publicly available as a modeling tool to study the impact of socio-economic differences and demographic heterogeneities across populations on the epidemiology of infectious diseases.

Statistical Analysis of Articles Published in China CDC Weekly - Worldwide, 2019-2020.

Introduction: This study analyzed views and downloads of articles published in China CDC Weekly from 2019 to 2020 as part of an evaluation of the academic level and quality of the journal. Methods: The study included articles published between November 29, 2019 and December 25, 2020 and evaluated views and downloads through February 9, 2021 using standard bibliometrics. We conducted network analysis with VOSviewer software. Results: There were 283 articles from 101 institutions published in China CDC Weekly during the analysis period, among which 22 (21.8%) institutions were overseas institutions. There were 220 unique first authors, with 1.28 articles per first author. There were 2,404,882 views and 58,760 downloads in total. The article with the highest view and download counts had 1,244,826 views and 38,978 downloads. Article types with more than 4,500 views per article were Vital Surveillance, Notes from the Field, and Preplanned Studies. Subjects with more than 3,500 views per article were epidemiology of infectious diseases, epidemiology of non-infectious diseases, and maternal and child health. Articles with descriptive research and articles discussing public health monitoring received more attention, shown by larger average per article page views. Discussion: Study results can help the editorial department improve the journal’s international influence through targeted measures, such as adjusting article types according to view and download analyses and increasing the proportion of international manuscripts selected.

One Health and Averting the Next Pandemic: Concept, Origin, Evolution, and Challenges

More than 70 percent of emerging human diseases are zoonotic (originate in animals). As of September 1, 2021, the ongoing pandemic (a global outbreak of a disease) caused by the novel coronavirus has infected more than 219 million people worldwide and caused more than 4.5 million deaths globally. The novel coronavirus pandemic may likely have its origin in animals before it was spilled over to the humans. As a public health professional and someone who has studied virus infections for a decade, my Infectious Disease Epidemiology course at the Texas A&M University School of Public Health had a focus on zoonotic diseases and the interconnections between animals, humans, and the environment. This article provides an overview of the recent zoonotic outbreaks, the concept of One Health, it's origins and evolution, and strides and challenges.

Addressing Sex and Gender Bias in COVID-19 Epidemiology in Bangladesh

Sex and gender are recognized as a vital factor in the infectious disease epidemiology, and disease outcomes, and these two factors also appear to hold for severe acute respiratory syndrome (SARS-CoV-2) infection. Evidence from COVID-19 infection in Bangladesh showed that a variation number of cases and deaths between the sex differences in immune responses to viruses and gender related risk factors among the male and female, but more severe outcomes in aged men of cases and deaths in 31~40 and 61~70 years respectively than female. However, the previous research dataset in the different parts of world evidenced that the men's are vulnerable compare to women's. Similar trends to observe in Bangladesh datasets in COVID-19 epidemiology. Male and female represented 71% and 29% of total reported confirmed COVID-19 cases in Bangladesh, respectively. Moreover, different levels of angiotensin converting enzyme 2 (ACE2) and transmembrane protease serine 2 (TMRSS2) enzymes play important role in COVID-19 infection of men and women. In addition, the effects of testosterone on ACE2 levels and the presence of ACE2 genes on the specific X-chromosome should not be ignored. In fine, this mini-review focuses on sex and gender variations in patients with an infectious disease of COVID-19 epidemiology in Bangladesh. The information of sex differences and age dependence might contribute to proper management and treatment of COVID-19 in Bangladesh.

Development of TaqMan Real-Time Polymerase Chain Reaction Assay for Detection of Chicken Anemia Virus in Newcastle Disease Vaccines.

Exogenous chicken anemia virus (CAV) has been detected in commercial poultry vaccines in various countries of the world. The presence of unwanted CAV in vaccines not only influences the epidemiology of chicken infectious anemia disease, but may also lead to vaccine failure and confusing results when vaccine responses are monitored. To detect CAV in contaminated vaccines, nucleic acid testing (unlike conventional testing) has a shorter processing time and does not require cell culture or live animals. The aim of the current study was to develop a TaqMan real-time polymerase chain reaction (PCR) assay to detect and quantify CAV in poultry vaccines and investigate CAV contamination in Razi live Newcastle disease vaccines. The TaqMan real-time PCR assay was set up, optimized, and validated in successive experiments. A standard plasmid pUC-VP2 containing viral protein 2 of CAV was constructed and used in the assay to generate a standard curve to quantify CAV genomes. A clear linear correlation was observed between threshold cycle (Ct) values and plasmid copy numbers in the amplification plots of 10-fold serial dilution of the plasmid. Total DNA of three samples of each of four different Razi live Newcastle disease vaccines, namely LaSota, B1, clone.12IR, and thermo-resistant strains, were extracted and subjected to real-time PCR assay. No CAV contamination was detected in the Razi Live Newcastle vaccines. The developed TaqMan real-time PCR assay provides a quick, specific, and sensitive method for use in detecting CAV in quality control vaccine testing and viral load studies.

Training tomorrow's doctors: the impact of a Student Selected Component in Global Health during medical school.

This article was migrated. The article was marked as recommended. Introduction:Several reports highlight the importance of global health education (GHE) for training tomorrow's doctors. In 2006, Newcastle University Medical School developed a Student Selected Component (SSC) in Global Health. We followed up students who completed the SSC to assess the impact on their experience as practising clinicians and postgraduate career development. Methods:We developed an electronic survey including questions about speciality choice, postgraduate qualifications, extracurricular activity and international work. Surveys were sent to 72 SSC participants identified between 2006-2017 through the Newcastle University Alumni and Supporters network and social media. Results: Surveys were returned by 37 (51%) SSC participants; 25 (71%) and 16 (46%) believed the SSC had influenced their clinical practice and career choice, respectively. Twenty-two (59%) obtained an intercalated degree programme, of whom nine (24%) did a Masters programme specifically in Global Health and four (11%), and two (5%) completed a Masters degree in Epidemiology and Control of Infectious Diseases respectively, both key themes within GHE. Four (11%) undertook, and 10 (29%) were considering postgraduate study related to global health, of whom three (9%) specified undertaking a Diploma in Tropical Medicine and Hygiene (DTM&H) and one (3%) studying a Masters degree in Public Health. Five (14%) had, and 19 (54%) were planning to work abroad, most referring to work in humanitarian or low resource settings and GHE programmes. Discussion and Conclusion:Participation in an SSC in Global Health may affect positive change in students' clinical practice and help inform academic and clinical career choice. Whilst a causative relationship cannot be inferred, the experience may support or increase the pursuit of additional global health-related qualifications, research and international health work. Medical schools that endeavour to produce graduates motivated to tackle our society's global health challenges should champion comprehensive global health modules for students.

Necrosecurity, Immunosupremacy, and Survivorship in the Political Imagination of COVID-19

Abstract The neologism ‘necrosecurity’ describes the cultural idea that mass death among less grievable subjects plays an essential role in maintaining social welfare and public order. In the early months of the novel coronavirus pandemic in the United States, this perspective on the social value of death emerged in diverse contexts, particularly in claims that deaths were a necessary consequence of returning economies to normal. Necrosecurity discourse encourages audiences to perceive coronavirus fatalities as neither preventable nor exceptional, and to perceive themselves as facing little risk of infection or death. Overlooking the realities of infectious disease epidemiology, these accounts portrayed COVID-19 as a mild disease and imagined a population of robust and physically normative individuals who would survive an epidemic unscathed and ready to return to work. These appeals articulate with powerful cultural tropes of survivorship, in which statistical calculations of relative risk and life chances—ostensibly cited to inspire hope for an individual outcome—conceal a zero-sum calculus in which ill or susceptible individuals are pitted against one another. In contrast to the construct of biosecurity—the securing of collective life against risk—necrosecurity paradoxically imagines the deaths of vulnerable others as a means of managing shared existential dangers.

Work, Health, and COVID-19

Work, Health, and COVID-19

Pokrovskiy Valentin Ivanovich

On October 29, 2020, the leader of Russian medicine, a great scientist and teacher, a truly great doctor, mentor of Russian infectious disease specialists and epidemiologists, the founder of a medical dynasty, advisor to the director for innovation of the Central Research Institute of Epidemiology of Rospotrebnadzor, professor, academician of the Russian Academy of Sciences Valentin Ivanovich Pokrovsky passed away.

Economic and Behavioral Influencers of Vaccination and Antimicrobial Use.

Despite vast improvements in global vaccination coverage during the last decade, there is a growing trend in vaccine hesitancy and/or refusal globally. This has implications for the acceptance and coverage of a potential vaccine against COVID-19. In the United States, the number of children exempt from vaccination for “philosophical belief-based” non-medical reasons increased in 12 of the 18 states that allowed this policy from 2009 to 2017 (1). Meanwhile, the overuse and misuse of antibiotics, especially in young children, have led to increasing rates of drug resistance that threaten our ability to treat infectious diseases. Vaccine hesitancy and antibiotic overuse exist side-by-side in the same population of young children, and it is unclear why one modality (antibiotics) is universally seen as safe and effective, while the other (vaccines) is seen as potentially hazardous by some. In this review, we consider the drivers shaping the use of vaccines and antibiotics in the context of three factors: individual incentives, risk perceptions, and social norms and group dynamics. We illustrate how these factors contribute to the societal and individual costs of vaccine underuse and antimicrobial overuse. Ultimately, we seek to understand these factors that are at the nexus of infectious disease epidemiology and social science to inform policy-making.

Covid-19 and the environment – the role of the Public Health Institute

The Croatian National Health Care Act defines the areas of activities of the public health institute, including the activities of the epidemiology of infectious diseases and chronic non-communicable diseases, public health, health promotion, environmental health, microbiology, school and adolescent medicine, mental health and addiction prevention at Zagreb City level. This paper reviews the highly variable activities in the Andrija Štampar Teaching Institute of Public Health with the aim of promoting a comprehensive approach to the COVID-19 pandemic. Human and analytical resources in the Institute, activities and rapid implementation of innovations testify to the high capacities for adaptation to emerging risks. In the Institute, it is possible to carry out a whole range of tests and to monitor the environmental factors with predominant impact on human health and safety of the Zagreb environment. The supply of safe water for human consumption in the Republic of Croatia during the current COVID-19 crisis has been uninterrupted and in accordance with applicable legislation. Also, our laboratories have been developing and introducing a method for wastewater testing for SARS-CoV-2 presence. The sludge from wastewater treatment plants is used in agriculture, and potential risks associated with the COVID-19 outbreak should be assessed prior to each application on the soil. Increased use of disinfectants during the epidemic may present a higher risk to the aquatic environment. Air quality monitoring indicates a positive impact on air quality as result of isolation measures.

Epidemiological trends of imported infectious diseases in Japan: Analysis of imported 2-year infectious disease registry data

IntroductionThe epidemiology of infectious diseases in Japan remains undefined despite the increasing tourism. GeoSentinel, an epidemiological surveillance system for reporting imported infectious diseases, has only two participating facilities in Japan. Although the number of infectious diseases is reported by the National Institute of Infectious Diseases, there is no detailed clinical information about these cases. Therefore, we established J-RIDA (Japan Registry for Infectious Diseases from Abroad) to clarify the status of imported infectious diseases in Japan and provide detailed information. MethodsJ-RIDA was started as a registry of imported infectious diseases. Case registration began in October 2017. Between October 2017 and September 2019, 15 medical institutions participated in this clinical study. The registry collected information about the patient's age, sex, nationality, chief complaint, consultation date, date of onset, whether visit was made to a travel clinic before travel, blood test results (if samples were collected), travel history, and final diagnosis. ResultsOf the 3046 cases included in this study, 46.7% to Southeast Asia, 13.0% to Africa, 13.7% to East Asia, 11.5% to South Asia, 7.5% to Europe, 3.8% to Central and South America, 4.6% to North America, 3.9% to Oceania, and 2.8% to Central and west Asia. More than 85% of chief complaints were fever and general symptoms, gastrointestinal symptoms, respiratory symptoms, or dermatologic problems. The most common diseases were travelers’ diarrhea, animal bite, upper respiratory infection, influenza, and dengue fever. ConclusionsWe summarized two-year cases registered in Japan's imported infectious disease registry. These results will significantly contribute to the epidemiology in Japan.

Covid‐19: Where We Are, What Got Us Here, and Where We Are Likely to Be Going—A Review Essay*

Covid‐19: Where We Are, What Got Us Here, and Where We Are Likely to Be Going—A Review Essay*

Detection of influenza epidemics using hidden Markov and Serfling approaches.

Detection of epidemics is a critical issue in epidemiology of infectious diseases which enable healthcare system to better control it. This study is devoted to investigating the 5-year trend in influenza and severe acute respiratory infection cases in Iran. The epidemics were also detected using the hidden Markov model (HMM) and Serfling model. In this study, we used SARI data reported in the World Health Organization (WHO) FluNet web-based tool from August 2011 to August 2016. SARI data in Iran from August 2011 to August 2016 were used. We applied the HMM and Serfling model for indicating the two epidemic and non-epidemic phases. The registered outbreak activity recorded on the WHO website was used as the gold standard. The coefficient of determination was reported to compare the goodness of fit of the models. Serfling models modified by 30% and 35% of the data had a sensitivity of 91.67% and 95.83%, while for 15%, 20% and 25% were 70.83%, 79.17% and 83.33%, respectively. Sensitivity of HMM and autoregressive HMM (AHMM) was 66.67% and 92.86%. All fitted models have a specificity of over 96%. The R2 for HMM and AHMM was calculated 0.73 and 0.85, respectively, showing better fitness of these models, while R2 was around 50% for different types of Serfling models. Both modified Serfling and HMM were acceptable models in determining the epidemic points for the detection of weekly SARI. The AHMM had better fitness, higher detection power and more accurate detection of the incidence of epidemics than Serfling model and high sensitivity and specificity. In addition to AHMM, Serfling models with 30% and 35% modification can be used to detect epidemics due to approximately the same accuracy but the simplicity of the calculations.

Lassa Fever: An Evolving Emergency in West Africa.

Lassa fever remains endemic in parts of West Africa and continues to pose as a quiescent threat globally. We described the background on Lassa fever, factors contributing to its emergence and spread, preventive measures, and potential solutions. This review provides a holistic and comprehensive source for academicians, clinicians, researchers, policymakers, infectious disease epidemiologists, virologists, and other stakeholders.

Infectious diseases epidemiology, quantitative methodology, and clinical research in the midst of the COVID-19 pandemic: Perspective from a European country

Starting from historic reflections, the current SARS-CoV-2 induced COVID-19 pandemic is examined from various perspectives, in terms of what it implies for the implementation of non-pharmaceutical interventions, the modeling and monitoring of the epidemic, the development of early-warning systems, the study of mortality, prevalence estimation, diagnostic and serological testing, vaccine development, and ultimately clinical trials. Emphasis is placed on how the pandemic had led to unprecedented speed in methodological and clinical development, the pitfalls thereof, but also the opportunities that it engenders for national and international collaboration, and how it has simplified and sped up procedures. We also study the impact of the pandemic on clinical trials in other indications. We note that it has placed biostatistics, epidemiology, virology, infectiology, and vaccinology, and related fields in the spotlight in an unprecedented way, implying great opportunities, but also the need to communicate effectively, often amidst controversy.