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Objectives: During June–July 2021, an outbreak of SARS-CoV-2 occurred among attendees of a summer youth camp in Nebraska. We assessed the factors that contributed to onward transmission of disease. Methods: The Four Corners Health Department conducted an outbreak investigation and recorded both laboratory-confirmed and self-reported cases of SARS-CoV-2 and mitigation measures employed. We generated sequences on positive specimens, created an epidemic curve to assist with outbreak visualization, and examined epidemiologic, genomic, and laboratory outcomes. Results: Evaluation of 3 index cases led to the identification of 25 people with COVID-19 who interacted directly with the camp. Contact tracing revealed an additional 18 cases consistent with onward community transmission. Most (24 of 35, 68.5%) vaccine-eligible community cases were not vaccinated. We sequenced 8 positive specimens; all were identified as the Delta variant. Precamp planning incorporated local health officials who recommended wearing face masks, practicing social distancing, and using attendee cohorts to limit mixing of people involved in various activities. Conclusion: Low vaccination levels and poor face mask–wearing habits among attendees resulted in secondary and tertiary spread of SARS-CoV-2 and severe outcomes among young adults. This outbreak of COVID-19 at a youth camp highlights the importance of vaccination and use of other measures to interrupt opportunities for SARS-CoV-2 spread in the community and shows that vaccinated people remain vulnerable to infection when in an environment of high exposure to SARS-CoV-2. Proactive case identification and interruption of chains of transmission can help decrease the number of cases and avoid further severe outcomes.

Background Aerosol transmission of COVID-19 is the subject of ongoing policy debate. Characterizing aerosol produced by people with COVID-19 is critical to understanding the role of aerosols in transmission. Objective We investigated the presence of virus in size-fractioned aerosols from six COVID-19 patients admitted into mixed acuity wards in April of 2020. Methods Size-fractionated aerosol samples and aerosol size distributions were collected from COVID-19 positive patients. Aerosol samples were analyzed for viral RNA, positive samples were cultured in Vero E6 cells. Serial RT-PCR of cells indicated samples where viral replication was likely occurring. Viral presence was also investigated by western blot and transmission electron microscopy (TEM). Results SARS-CoV-2 RNA was detected by rRT-PCR in all samples. Three samples confidently indicated the presence of viral replication, all of which were from collected sub-micron aerosol. Western blot indicated the presence of viral proteins in all but one of these samples, and intact virions were observed by TEM in one sample. Significance Observations of viral replication in the culture of submicron aerosol samples provides additional evidence that airborne transmission of COVID-19 is possible. These results support the use of efficient respiratory protection in both healthcare and by the public to limit transmission.

Health events emerge from host, community, environment, and pathogen factors—forecasting epidemics is a complex task. We describe an exploratory analysis to identify economic risk factors that could aid epidemic risk assessment. A line list was constructed using the World Health Organization Disease Outbreak News (2016–2018) and economic indicators from the World Bank. Poisson regression employing forward imputations was used to establish relationships with the frequency with which countries reported public health events. Economic indicators demonstrated strong performance appropriate for further assessment in surveillance programming. In our analysis, three economic indicators were significantly associated to event reporting: how much the country’s urban population changed, its average forest area, and a novel economic indicator we developed that assessed how much the gross domestic product changed per capita. Other economic indicators performed less well: changes in total, female, urban, and rural population sizes; population density; net migration; change in per cent forest area; total forest area; and another novel indicator, change in percent of trade as a fraction of the total economy. We then undertook a further analysis of the start of the current COVID-19 pandemic that revealed similar associations, but confounding by global disease burden is likely. Continued development of forecasting approaches capturing information relevant to whole-of-society factors (e.g., economic factors as assessed in our study) could improve the risk management process through earlier hazard identification and inform strategic decision processes in multisectoral strategies to preventing, detecting, and responding to pandemic-threat events.

We conducted an assessment of disability, anxiety, and other life impacts of COVID-19 and isolation care in a unique cohort of individuals. These included both community admissions to a university hospital as well as some of the earliest international aeromedical evacuees. Among an initial 16 COVID-19 survivors that were interviewed 6–12 months following their admission into isolation care, perception of their isolation care experience was related to their reporting of long-term consequences. However, anxiety and disability assessed with standard scores had no relationship with each other. Both capture of the isolation care experience and caution relying on single scoring systems for assessing long-term consequences in survivors are important considerations for on-going and future COVID-19 and other pandemic survivor research.

Mass gatherings have been implicated in higher rates of transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), and many sporting events have been restricted or canceled to limit disease spread (1). Based on current CDC COVID-19 mitigation recommendations related to events and gatherings (2), Major League Baseball (MLB) developed new health and safety protocols before the July 24 start of the 2020 season. In addition, MLB made the decision that games would be played without spectators. Before a three-game series between teams A and B, the Philadelphia Department of Public Health was notified of a team A player with laboratory-confirmed COVID-19; the player was isolated as recommended (2). During the series and the week after, laboratory-confirmed COVID-19 was diagnosed among 19 additional team A players and staff members and one team B staff member. Throughout their potentially infectious periods, some asymptomatic team A players and coaches, who subsequently received positive SARS-CoV-2 test results, engaged in on-field play with teams B and C. No on-field team B or team C players or staff members subsequently received a clinical diagnosis of COVID-19. Certain MLB health and safety protocols, which include frequent diagnostic testing for rapid case identification, isolation of persons with positive test results, quarantine for close contacts, mask wearing, and social distancing, might have limited COVID-19 transmission between teams.

The optimal time to initiate research on emergencies is before they occur. However, timely initiation of high-quality research may launch during an emergency under the right conditions. These include an appropriate context, clarity in scientific aims, preexisting resources, strong operational and research structures that are facile, and good governance. Here, Nebraskan rapid research efforts early during the 2020 coronavirus disease pandemic, while participating in the first use of U.S. federal quarantine in 50 years, are described from these aspects, as the global experience with this severe emerging infection grew apace. The experience has lessons in purpose, structure, function, and performance of research in any emergency, when facing any threat.

Objectives: This is a protocol for a Cochrane Review (intervention). The objectives are as follows:. To assess the beneficial and harmful effects of antibiotics versus placebo, no intervention, or another antibiotic for the treatment of people with leptospirosis.

Nigeria struggles with seasonal outbreaks of Lassa fever (LF), with 70 to 100% of its states affected annually. Since 2018, the seasonal dynamics have changed with a stark increase in infections, though the pattern in 2021 differed from the other years. Nigeria had three outbreaks of Lassa Fever in 2021. In that year, Nigeria also experienced substantial burdens from COVID-19 and Cholera. There is potential that these three outbreak events interacted with each other. This may have been from community disruption and so changes in how people access the health system, how the health system responds, or overlapping biological interactions, misclassification, social factors, misinformation, and pre-existing disparities and vulnerabilities. We assessed the syndemic potential of Lassa Fever, COVID-19, and Cholera through modeling their interactions across the 2021 calendar year employing a Poisson regression model. We included the number of states affected and the month of the year. We used these predictors to forecast the progression of the outbreak using a Seasonal Autoregressive Integrated Moving Average (SARIMA) model. The Poisson model prediction for the confirmed number of Lassa fever cases was significantly dependent on the number of confirmed COVID-19 cases, the number of states affected, and the month of the year (p-value < 0.001), and the SARIMA model was a good fit, accounting for 48% of the change in the number of cases of Lassa fever (p-value < 0.001) with parameters ARIMA (6, 1, 3) (5, 0, 3). Lassa Fever, COVID-19, and Cholera 2021 case curves have mirrored dynamics and likely interact. Further research into common, intervenable aspects of those interactions should be performed.

Objectives: This is a protocol for a Cochrane Review (intervention). The objectives are as follows:. To assess the beneficial and harmful effects of antibiotics for the prevention of leptospirosis.

Background The importance of infectious disease epidemic forecasting and prediction research is underscored by decades of communicable disease outbreaks, including COVID-19. Unlike other fields of medical research, such as clinical trials and systematic reviews, no reporting guidelines exist for reporting epidemic forecasting and prediction research despite their utility. We therefore developed the EPIFORGE checklist, a guideline for standardized reporting of epidemic forecasting research. Methods and findings We developed this checklist using a best-practice process for development of reporting guidelines, involving a Delphi process and broad consultation with an international panel of infectious disease modelers and model end users. The objectives of these guidelines are to improve the consistency, reproducibility, comparability, and quality of epidemic forecasting reporting. The guidelines are not designed to advise scientists on how to perform epidemic forecasting and prediction research, but rather to serve as a standard for reporting critical methodological details of such studies. Conclusions These guidelines have been submitted to the EQUATOR network, in addition to hosting by other dedicated webpages to facilitate feedback and journal endorsement., Simon Pollett and co-workers describe EPIFORGE, a guideline for reporting research on epidemic forecasting.

Key Points Question Does weekly testing of kindergarten through 12th grade students and staff improve detection of SARS-CoV-2 infection and understanding of the epidemiology of SARS-CoV-2 in urban public school settings? Findings In this quality improvement study, weekly school-based saliva polymerase chain reaction testing at 3 urban public schools was associated with increased case detection among staff and students compared with symptom-based strategies, exceeding county-level case rates. SARS-CoV-2 was detected in school wastewater samples each week as well as air and surface samples from choir classrooms. Meaning This study suggests that routine SARS-CoV-2 testing may identify infected staff and students who are not identified through conventional case detection and may provide insight into disease burdens of undertested communities., Importance Scalable programs for school-based SARS-CoV-2 testing and surveillance are needed to guide in-person learning practices and inform risk assessments in kindergarten through 12th grade settings. Objectives To characterize SARS-CoV-2 infections in staff and students in an urban public school setting and evaluate test-based strategies to support ongoing risk assessment and mitigation for kindergarten through 12th grade in-person learning. Design, Setting, and Participants This pilot quality improvement program engaged 3 schools in Omaha, Nebraska, for weekly saliva polymerase chain reaction testing of staff and students participating in in-person learning over a 5-week period from November 9 to December 11, 2020. Wastewater, air, and surface samples were collected weekly and tested for SARS-CoV-2 RNA to evaluate surrogacy for case detection and interrogate transmission risk of in-building activities. Main Outcomes and Measures SARS-CoV-2 detection in saliva and environmental samples and risk factors for SARS-CoV-2 infection. Results A total of 2885 supervised, self-collected saliva samples were tested from 458 asymptomatic staff members (mean [SD] age, 42.9 [12.4] years; 303 women [66.2%]; 25 Black or African American [5.5%], 83 Hispanic [18.1%], 312 White [68.1%], and 35 other or not provided [7.6%]) and 315 students (mean age, 14.2 [0.7] years; 151 female students [48%]; 20 Black or African American [6.3%], 201 Hispanic [63.8%], 75 White [23.8%], and 19 other race or not provided [6.0%]). A total of 46 cases of SARS-CoV-2 (22 students and 24 staff members) were detected, representing an increase in cumulative case detection rates from 1.2% (12 of 1000) to 7.0% (70 of 1000) among students and from 2.1% (21 of 1000) to 5.3% (53 of 1000) among staff compared with conventional reporting mechanisms during the pilot period. SARS-CoV-2 RNA was detected in wastewater samples from all pilot schools as well as in air samples collected from 2 choir rooms. Sequencing of 21 viral genomes in saliva specimens demonstrated minimal clustering associated with 1 school. Geographical analysis of SARS-CoV-2 cases reported district-wide demonstrated higher community risk in zip codes proximal to the pilot schools. Conclusions and Relevance In this study of staff and students in 3 urban public schools in Omaha, Nebraska, weekly screening of asymptomatic staff and students by saliva polymerase chain reaction testing was associated with increased SARS-CoV-2 case detection, exceeding infection rates reported at the county level. Experiences differed among schools, and virus sequencing and geographical analyses suggested a dynamic interplay of school-based and community-derived transmission risk. Collectively, these findings provide insight into the performance and community value of test-based SARS-CoV-2 screening and surveillance strategies in the kindergarten through 12th grade educational setting., This quality improvement study characterizes SARS-CoV-2 infections in staff and students in an urban public school setting and evaluates test-based strategies to support ongoing risk assessment and mitigation for kindergarten through 12th grade in-person learning.

In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.

As the coronavirus disease 2019 (COVID-19) continues to circulate, testing strategies are of the utmost importance. Given national shortages of testing supplies, personal protective equipment, and other hospital resources, diagnostic stewardship is necessary to aid in resource management. We report the low utility of serial testing in a low-prevalence setting.

The current strategy used by many funding agencies for determining how money is spent on research to help prevent infectious disease outbreaks is based on pathogen-specific priority lists. Listing disease threats provides focus for business and research planning conducive to specific goals of developing a drug, or a vaccine, or other particular product. But, this singular type of focus has consequences. This perspective explores the consequences of lists, and describes how parallel programming independent of disease lists that address what we need to do to prevent and mitigate emerging disease risks may provide benefits out of reach of a singular focus on what products we need to have.

Background: Observed COVID-19 cases and deaths are frequently used as independent factors to justify the use or de-escalation of non-pharmaceutical interventions. To investigate and describe the temporal relationship between changes in epidemic curves for COVID-19 cases and deaths, a longitudinal analysis of these metrics was performed for 16 states in the United States and three countries.Results: The analysis performed demonstrates a considerable, consistent lag between a surge in COVID-19 cases and the subsequent rise in attributable deaths, with approximately a month-long lag observed.Conclusions: The time lag identified must be incorporated in health emergency decision making in order to avoid the pre-mature de-escalation of disease mitigation measures.

ImportanceScalable programs for school-based SARS-CoV-2 testing and surveillance are needed to guide in-person learning practices and inform risk assessments in K-12 settings.ObjectivesTo characterize SARS-CoV-2 infections in staff and students in an urban public school setting and evaluate test-based strategies to support ongoing risk assessment and mitigation for K-12 in-person learning.Design, Setting, and ParticipantsThe pilot program engaged three schools for weekly saliva PCR testing of staff and students participating in in-person learning over a 5-week period. Wastewater, air, and surface samples were collected weekly and tested for SARS-CoV-2 RNA to determine surrogacy for case detection and interrogate transmission risk of in-building activities.Main Outcomes and MeasuresSARS-CoV-2 detection in saliva and environmental samples and risk factors for SARS-CoV-2 infection.Results2,885 supervised self-collected saliva samples were tested from 773 asymptomatic staff and students during November and December, 2020. 46 cases (22 students, 24 staff) were detected, representing a 5.8- and 2.5-fold increase in case detection rates among students and staff, respectively, compared to conventional reporting mechanisms. SARS-CoV-2 RNA was detected in wastewater samples from all pilot schools, as well as in air samples collected from two choir rooms. Sequencing of 21 viral genomes in saliva specimens demonstrated minimal clustering associated with one school. Geographic analysis of SARS-CoV-2 cases reported district-wide demonstrated higher community risk in zip codes proximal to the pilot schools.Conclusions and RelevanceWeekly screening of asymptomatic staff and students by saliva PCR testing dramatically increased SARS-CoV-2 case detection in an urban public-school setting, exceeding infection rates reported at the county level. Experiences differed among schools, and virus sequencing and geographic analyses suggest a dynamic interplay of school-based and community-derived transmission risk. Environmental testing for SARS-CoV-2 RNA in air and surface samples enabled real-time risk assessment of in-school activities and allowed for interventions in choir classes. Wastewater testing demonstrated the utility of school building-level SARS-CoV-2 surveillance. Collectively, these findings provide insight into the performance and community value of test-based SARS-CoV-2 screening and surveillance strategies in the K-12 educational setting.KEY POINTSQuestionDo test-based programs reduce SARS-CoV-2 risk in K-12 schools?FindingsWeekly school-based saliva PCR testing at three urban public schools doubled case detection among staff and students over symptom-based strategies, exceeding county-level case rates. SARS-CoV-2 was detected in school wastewater samples each week, as well as air and surface samples related to choir classrooms.MeaningRoutine SARS-CoV-2 testing removes infected staff and students from school who are not identified through conventional case detection. With rigorous infection control and environmental monitoring, this helps mitigate risk during school operations. Furthermore, screening in K-12 schools may provide insight into disease burdens of undertested communities.

Background Balancing the use of antibacterial therapy against selection for resistance in this pandemic era has introduced both questions and guidelines. In this project, we explored how prescription of empirical antibacterial therapy differs between those with and without SARS-CoV-2 infection. Methods Multivariable logistic regression was used to determine whether COVID-19 status and other factors play a role in the prescription of antibacterial therapy in an inpatient setting at a large referral academic medical centre. Further analysis was conducted to determine whether these factors differ between those testing positive and negative for SARS-CoV-2. Results Of 405 patients in the cohort, 175 received antibacterial therapy and 296 tested positive for SARS-CoV-2. A positive SARS-CoV-2 test carried an OR of 0.3 (95% CI: 0.19, 0.49) for receiving antibacterial treatment in the first 48 h after admission (P Conclusions Antibacterial therapy prescription differs by COVID-19 disease status, and procalcitonin results are most highly associated with antibacterial use across strata.

ObjectivesThis systematic review and meta-analysis synthesized the evidence on the impact of demographics and comorbidities with clinical outcomes of COVID-19, including severe illness, admission to the intensive care unit (ICU), and death.MethodsThe PRISMA guidelines were followed to conduct and report this meta-analysis. The protocol is registered in PROSPERO International prospective register of systematic reviews (ID=CRD42020184440). Two authors independently searched literature from PubMed, Embase, Cochrane library and CINHAL on May 6, 2020; removed duplicates; screened titles, abstracts and full text using criteria; and extracted data from eligible articles. A random-effects model was used to estimate the summary odds ratio (OR). Variations among studies were examined using Cochrane Q and I2.ResultsOut of 4,275 articles obtained from the databases and screened, 71 studies that involved 216,843 patients were abstracted and then, where appropriate, analyzed by meta-analysis. The COVID-19 related outcomes reported were death in 26 studies, severe illness in 41 studies, and admission to ICU in 11 studies. Death was significantly correlated with hypertension (OR 2.60, 95% CI 1.95–3.25, I2 = 52.6%, n= 13 studies), cardiovascular disease (5.16, 4.10–6.22, 0.0%, 6), diabetes (2.11, 1.35–2.87, 67.4%, 12), chronic respiratory disease (2.83, 2.14–3.51, 0.0%, 9), cerebrovascular diseases (5.14, 1.08–9.19, 0.0%, 2), male sex (1.34, 1.18 1.50, 38.7%, 16), age older than 60 (6.09, 3.53 8.66, 95.5%, 6) or 65 years (3.56, 1.21 5.90, 18.2%, 6). Severe illness was also significantly associated with hypertension (1.70, 1.30 –2.10, 47.8%, 21), cardiovascular diseases (2.04, 1.01–3.08, 30.6%, 10), diabetes (1.65, 1.23–2.08, 24.9%, 18), male sex (1.35, 1.23 1.47, 0.0%, 32) and age at least 60 (4.91, 1.35 8.47, 0.0%, 4) or 65 (2.55,1.94 3.17, 24.5%, 9) years. Among hospitalized patients, the odds of admission to ICU was greater in individuals who had cardiovascular diseases (1.36,1.04–1.69, 0.0%, 4), diabetes (1.55, 1.20–1.90, 0.0%, 5) and chronic respiratory disease (1.52, 1.09–1.94, 0.0%, 5) than those who were not having these comorbidities.ConclusionsOlder age and chronic diseases increase the risk of developing severe illness, admission to ICU and death among COVID-19 patients. Special strategies are warranted to prevent SARS-CoV-2 infection and manage COVID-19 cases in those with vulnerabilities.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan, China in late 2019, and its resulting coronavirus disease, COVID-19, was declared a pandemic by the World Health Organization on March 11, 2020. The rapid global spread of COVID-19 represents perhaps the most significant public health emergency in a century. As the pandemic progressed, a continued paucity of evidence on routes of SARS-CoV-2 transmission has resulted in shifting infection prevention and control guidelines between classically-defined airborne and droplet precautions. During the initial isolation of 13 individuals with COVID-19 at the University of Nebraska Medical Center, we collected air and surface samples to examine viral shedding from isolated individuals. We detected viral contamination among all samples, supporting the use of airborne isolation precautions when caring for COVID-19 patients.

Natural disasters, disease outbreaks, famine, and human conflict have strained communities everywhere over the course of human existence. However, modern changes in climate, human mobility, and other factors have increased the global community's vulnerability to widespread emergencies. We are in the midst of a disruptive health event, with the COVID‐19 pandemic testing our health provider systems globally. This study presents a qualitative analysis of published literature, obtained systematically, to examine approaches health providers are taking to prepare for and respond to mass casualty incidents around the globe. The research reveals emerging trends in the weaknesses of systems' disaster responses while highlighting proposed solutions, so that others may better prepare for future disasters. Additionally, the research examines gaps in the literature, to foster more targeted and actionable contributions to the literature., Key Points The literature is saturated with needs assessments for disaster training and primary reports following disasters. More research addressing innovation in hospital disaster simulation, protocols, post‐acute response and supply, and staffing is warranted.More quantitative research is needed, particularly showing mortality and morbidity outcomes from disaster interventions at the provider and hospital system level.Common shortcomings in hospital disaster plans are telecommunication failure, plans for surge capacity, insufficient stockpiles, coordination with other hospitals/disaster responders, and staff knowledge of disaster protocols.Hospital system leadership should plan for the repercussions of disruptions in usual care during the disaster, such as chronic disease exacerbation and new acute infections during recovery.Healthcare providers and staff are vulnerable to psychological strain, particularly during infectious disease outbreaks, and this should be addressed early and aggressively.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission causing coronavirus disease 2019 (COVID-19) may occur through multiple routes. We collected aerosol samples around six patients admitted into mixed acuity wards in April of 2020 to identify the risk of airborne SARS-CoV-2. Measurements were made to characterize the size distribution of aerosol particles, and size-fractionated, aerosol samples were collected to assess the presence of infectious virus in particles sizes of >4.1 µm, 1-4 µm, and 4.1 µm, 1-4 µm, and

ObjectivesHealth events emerge from a multifactorial milieu involving host, community, environment, and pathogen factors. Therefore, developing accurate forecasting models to improve epidemic prediction towards better prevention and capabilities management is a complex task. Here, we describe an exploratory analysis to identify non-health risk factors that could improve the forecast and events risk signals using a feasible and practical approach by combining surveillance report data with non-health data from open data sources.MethodsA line listing was developed using information from the World Health Organization Disease Outbreaks News from 2016-2018. A database was created merging the line listing data with non-health indicators from the World Bank. Poisson regression models employing forward imputations were used to establish relationships and predict values over the dependent variable (health event frequency); which are the health events reported by each country to WHO during 2016-2018.FindingsThe resulting regression model provided evidence that changes in non-health factors important to community experiences impact the risk of the number of major health events that a country could experience. Three non-health indicators (extrinsic factors) were associated significantly to event frequency (population urban change, gross domestic product change per capita—a novel factor, and average forest area). An exploratory analysis of the current COVID-19 pandemic suggested similar associations, but confounding by global disease burden is likely.ConclusionContinued development of forecasting approaches capturing available whole-of-society extrinsic factors (non-health factors); could improve the risk management process through earlier hazard identification, and as importantly inform strategic decision processes in multisectoral strategies to preventing, detecting, and responding to pandemic-threat events.

The Deployment and Travel Medicine Knowledge, Attitudes, Practices, and Outcomes Study (KAPOS) examines the integrated relationship between provider and patient inputs and health outcomes associated with travel and deployments. This study describes malaria chemoprophylaxis prescribing patterns by medical providers within the U.S. Department of Defense’s Military Health System and its network of civilian healthcare providers during a 5-year period. Chemoprophylaxis varied by practice setting, beneficiary status, and providers’ travel medicine expertise. Whereas both civilian and military facilities prescribe an increasing proportion of atovaquone–proguanil, doxycycline remains the most prevalent antimalarial at military facility based practices. Civilian providers dispense higher rates of mefloquine than their military counterparts. Within military treatment facilities, travel medicine specialists vary their prescribing pattern based on service member versus beneficiary status of the patient, both in regards to primary prophylaxis, and use of presumptive anti-relapse therapy (PQ-PART). By contrast, nonspecialists appear to carry over practice patterns developed under force health protection (FHP) policy for service members, into the care of beneficiaries, particularly in high rates of prescribing doxycycline and PQ-PART compared with both military travel medicine specialists and civilian comparators. Force health protection policy plays an important role in standardizing and improving the quality of care for deployed service members, but this may not be the perfect solution outside of the deployment context. Solutions that broaden both utilization of decision support tools and travel medicine specialty care are necessary.

The West Africa Ebola virus disease outbreak of 2014-2016 demonstrated that responses to viral hemorrhagic fever epidemics must go beyond emergency stopgap measures and should incorporate high-quality medical care and clinical research. Optimal patient management is essential to improving outcomes, and it must be implemented regardless of geographical location or patient socioeconomic status. Coupling clinical research with improved care has a significant added benefit: Improved data quality and management can guide the development of more effective supportive care algorithms and can support regulatory approvals of investigational medical countermeasures (MCMs), which can alter the cycle of emergency response to reemerging pathogens. However, executing clinical research during outbreaks of high-consequence pathogens is complicated and comes with ethical and research regulatory challenges. Aggressive care and excellent quality control must be balanced by the requirements of an appropriate infection prevention and control posture for healthcare workers and by overcoming the resource limitations inherent in many outbreak settings. The Joint Mobile Emerging Disease Intervention Clinical Capability was established in 2015 to develop a high-quality clinical trial capability in Uganda to support rigorous evaluation of MCMs targeting high-consequence pathogens like Ebola virus. This capability assembles clinicians, laboratorians, clinical researchers, logisticians, and regulatory professionals trained in infection prevention and control and in good clinical and good clinical laboratory practices. The resulting team is prepared to provide high-quality medical care and clinical research during high-consequence outbreaks.

BACKGROUND Computed tomography (CT) scans are increasingly available in clinical care globally. They enable a rapid and detailed assessment of tissue and organ involvement in disease processes that are relevant to diagnosis and management, particularly in the context of the COVID-19 pandemic. OBJECTIVE The aim of this paper is to identify differences in the CT scan findings of patients who were COVID-19 positive (confirmed via nucleic acid testing) to patients who were confirmed COVID-19 negative. METHODS A retrospective cohort study was proposed to compare patient clinical characteristics and CT scan findings in suspected COVID-19 cases. A multivariable logistic model with LASSO (least absolute shrinkage and selection operator) selection for variables was used to identify the good predictors from all available predictors. The area under the curve (AUC) with 95% CI was calculated for each of the selected predictors and the combined selected key predictors based on receiver operating characteristic curve analysis. RESULTS A total of 94 (56%) patients were confirmed positive for COVID-19 from the suspected 167 patients. We found that elderly people were more likely to be infected with COVID-19. Among the 94 confirmed positive patients, 2 (2%) patients were admitted to an intensive care unit. No patients died during the study period. We found that the presence, distribution, and location of CT lesions were associated with the presence of COVID-19. White blood cell count, cough, and a travel history to Wuhan were also the top predictors for COVID-19. The overall AUC of these selected predictors is 0.97 (95% CI 0.93-1.00). CONCLUSIONS Taken together with nucleic acid testing, we found that CT scans can allow for the rapid diagnosis of COVID-19. This study suggests that chest CT scans should be more broadly adopted along with nucleic acid testing in the initial assessment of suspected COVID-19 cases, especially for patients with nonspecific symptoms.

Background Computed tomography (CT) scans are increasingly available in clinical care globally. They enable a rapid and detailed assessment of tissue and organ involvement in disease processes that are relevant to diagnosis and management, particularly in the context of the COVID-19 pandemic. Objective The aim of this paper is to identify differences in the CT scan findings of patients who were COVID-19 positive (confirmed via nucleic acid testing) to patients who were confirmed COVID-19 negative. Methods A retrospective cohort study was proposed to compare patient clinical characteristics and CT scan findings in suspected COVID-19 cases. A multivariable logistic model with LASSO (least absolute shrinkage and selection operator) selection for variables was used to identify the good predictors from all available predictors. The area under the curve (AUC) with 95% CI was calculated for each of the selected predictors and the combined selected key predictors based on receiver operating characteristic curve analysis. Results A total of 94 (56%) patients were confirmed positive for COVID-19 from the suspected 167 patients. We found that elderly people were more likely to be infected with COVID-19. Among the 94 confirmed positive patients, 2 (2%) patients were admitted to an intensive care unit. No patients died during the study period. We found that the presence, distribution, and location of CT lesions were associated with the presence of COVID-19. White blood cell count, cough, and a travel history to Wuhan were also the top predictors for COVID-19. The overall AUC of these selected predictors is 0.97 (95% CI 0.93-1.00). Conclusions Taken together with nucleic acid testing, we found that CT scans can allow for the rapid diagnosis of COVID-19. This study suggests that chest CT scans should be more broadly adopted along with nucleic acid testing in the initial assessment of suspected COVID-19 cases, especially for patients with nonspecific symptoms.

Lack of evidence on SARS-CoV-2 transmission dynamics has led to shifting isolation guidelines between airborne and droplet isolation precautions. During the initial isolation of 13 individuals confirmed positive with COVID-19 infection, air and surface samples were collected in eleven isolation rooms to examine viral shedding from isolated individuals. While all individuals were confirmed positive for SARS-CoV-2, symptoms and viral shedding to the environment varied considerably. Many commonly used items, toilet facilities, and air samples had evidence of viral contamination, indicating that SARS-CoV-2 is shed to the environment as expired particles, during toileting, and through contact with fomites. Disease spread through both direct (droplet and person-to-person) as well as indirect contact (contaminated objects and airborne transmission) are indicated, supporting the use of airborne isolation precautions.One Sentence SummarySARS-CoV-2 is shed during respiration, toileting, and fomite contact, indicating that infection may occur in both direct and indirect contact.

International travel continues to increase in numbers and complexity. Despite the availability of pretravel health advice, travelers remain at risk for exposure to common organisms as well as emerging pathogens. With low rates of travel clinic utilization, it is important for the general practitioner to remain aware of the importance of travel health, risk factors unique to individual patients, and evolving threats. This review highlights important considerations when evaluating ill travelers, incorporating emerging infectious threats.

Introduction: The Ebola virus disease (EVD) outbreak in Nigeria began when an infected diplomat from Liberia arrived in Lagos, the most populous city in Africa, with subsequent transmission to another large city. Methods: First-, second-, and third-generation contacts were traced, monitored, and classified. Symptomatic contacts were managed at Ebola treatment centers as suspected, probable, and confirmed EVD cases using standard operating procedures adapted from the World Health Organization EVD guidelines. Reverse transcription PCR tests confirmed EVD. Socio-demographic, clinical, hospitalization, and outcome data of the July–September 2014 Nigeria EVD cohort were analyzed. Results: The median age of the 20 EVD cases was 33 years (interquartile range 26–62 years). More females (55%), health workers (65%), and persons

Health workers infected with Ebola virus in Kenema, Sierra Leone, had potential virus exposure inside and outside of hospitals. Prevention measures must address a spectrum of risk factors both in formal and informal care settings as well as in the community., Background. Ebola virus disease (EVD) in health workers (HWs) has been a major challenge during the 2014–2015 outbreak. We examined factors associated with Ebola virus exposure and mortality in HWs in Kenema District, Sierra Leone. Methods. We analyzed data from the Sierra Leone National Viral Hemorrhagic Fever Database, contact tracing records, Kenema Government Hospital (KGH) staff and Ebola Treatment Unit (ETU) rosters, and burial logs. Results. From May 2014 through January 2015, 600 cases of EVD originated in Kenema District, including 92 (15%) HWs, 66 (72%) of whom worked at KGH. Among KGH medical staff and international volunteers, 18 of 62 (29%) who worked in the ETU developed EVD, compared with 48 of 83 (58%) who worked elsewhere in the hospital. Thirteen percent of HWs with EVD reported contact with EVD patients, while 27% reported contact with other infected HWs. The number of HW EVD cases at KGH declined roughly 1 month after implementation of a new triage system at KGH and the opening of a second ETU within the district. The case fatality ratio for HWs and non-HWs with EVD was 69% and 74%, respectively. Conclusions. The cluster of HW EVD cases in Kenema District is one of the largest ever reported. Most HWs with EVD had potential virus exposure both inside and outside of hospitals. Prevention measures for HWs must address a spectrum of infection risks in both formal and informal care settings as well as in the community.

NGR reports funding by NIGMS grant R35GM119582. BMA is supported by Bill and Melinda Gates Foundation through the Global Good Fund. SP and IMB were funded by the Armed Forces Health Surveillance Branch (GEIS: P0116_19_WR_03.11). Introduction: High quality epidemic forecasting and prediction are critical to support response to local, regional and global infectious disease threats. Other fields of biomedical research use consensus reporting guidelines to ensure standardization and quality of research practice among researchers, and to provide a framework for end-users to interpret the validity of study results. The purpose of this study was to determine whether guidelines exist specifically for epidemic forecast and prediction publications. Methods: We undertook a formal systematic review to identify and evaluate any published infectious disease epidemic forecasting and prediction reporting guidelines. This review leveraged a team of 18 investigators from US Government and academic sectors. Results: A literature database search through May 26, 2019, identified 1467 publications (MEDLINE n = 584, EMBASE n = 883), and a grey-literature review identified a further 407 publications, yielding a total 1777 unique publications. A paired-reviewer system screened in 25 potentially eligible publications, of which two were ultimately deemed eligible. A qualitative review of these two published reporting guidelines indicated that neither were specific for epidemic forecasting and prediction, although they described reporting items which may be relevant to epidemic forecasting and prediction studies. Conclusions: This systematic review confirms that no specific guidelines have been published to standardize the reporting of epidemic forecasting and prediction studies. These findings underscore the need to develop such reporting guidelines in order to improve the transparency, quality and implementation of epidemic forecasting and prediction research in operational public health. Publisher PDF

BACKGROUND: Computed tomography (CT) scans are increasingly available in clinical care globally. They enable a rapid and detailed assessment of tissue and organ involvement in disease processes that are relevant to diagnosis and management, particularly in the context of the COVID-19 pandemic. OBJECTIVE: The aim of this paper is to identify differences in the CT scan findings of patients who were COVID-19 positive (confirmed via nucleic acid testing) to patients who were confirmed COVID-19 negative. METHODS: A retrospective cohort study was proposed to compare patient clinical characteristics and CT scan findings in suspected COVID-19 cases. A multivariable logistic model with LASSO (least absolute shrinkage and selection operator) selection for variables was used to identify the good predictors from all available predictors. The area under the curve (AUC) with 95% CI was calculated for each of the selected predictors and the combined selected key predictors based on receiver operating characteristic curve analysis. RESULTS: A total of 94 (56%) patients were confirmed positive for COVID-19 from the suspected 167 patients. We found that elderly people were more likely to be infected with COVID-19. Among the 94 confirmed positive patients, 2 (2%) patients were admitted to an intensive care unit. No patients died during the study period. We found that the presence, distribution, and location of CT lesions were associated with the presence of COVID-19. White blood cell count, cough, and a travel history to Wuhan were also the top predictors for COVID-19. The overall AUC of these selected predictors is 0.97 (95% CI 0.93-1.00). CONCLUSIONS: Taken together with nucleic acid testing, we found that CT scans can allow for the rapid diagnosis of COVID-19. This study suggests that chest CT scans should be more broadly adopted along with nucleic acid testing in the initial assessment of suspected COVID-19 cases, especially for patients with nonspecific symptoms.

Infectious disease modeling has played a prominent role in recent outbreaks, yet integrating these analyses into public health decision-making has been challenging. We recommend establishing ‘outbreak science’ as an inter-disciplinary field to improve applied epidemic modeling.

Introduction Knowledge of the contemporary epidemiology of hepatitis B virus (HBV) infection among military personnel can inform potential Department of Defense (DoD) screening policy and infection and disease control strategies. Materials and Methods HBV infection status at accession and following deployment was determined by evaluating reposed serum from 10,000 service members recently deployed to combat operations in Iraq and Afghanistan in the period from 2007 to 2010. A cost model was developed from the perspective of the Department of Defense for a program to integrate HBV infection screening of applicants for military service into the existing screening program of screening new accessions for vaccine-preventable infections. Results The prevalence of chronic HBV infection at accession was 2.3/1,000 (95% CI: 1.4, 3.2); most cases (16/21, 76%) identified after deployment were present at accession. There were 110 military service-related HBV infections identified. Screening accessions who are identified as HBV susceptible with HBV surface antigen followed by HBV surface antigen neutralization for confirmation offered no cost advantage over not screening and resulted in a net annual increase in cost of $5.78 million. However, screening would exclude as many as 514 HBV cases each year from accession. Conclusions Screening for HBV infection at service entry would potentially reduce chronic HBV infection in the force, decrease the threat of transfusion-transmitted HBV infection in the battlefield blood supply, and lead to earlier diagnosis and linkage to care; however, applicant screening is not cost saving. Service-related incident infections indicate a durable threat, the need for improved laboratory-based surveillance tools, and mandate review of immunization policy and practice.

The analysis of HIV-1 sequences has helped understand the viral molecular epidemiology, monitor the development of antiretroviral drug resistance, and design candidate vaccines. The introduction of single genome amplification (SGA) has been a major advancement in the field, allowing for the characterization of multiple sequences per patient while preserving linkage among polymorphisms in the same viral genome copy. Sequencing of SGA amplicons is performed by capillary Sanger sequencing, which presents low throughput, requires a high amount of template, and is highly sensitive to template/primer mismatching. In order to meet the increasing demand for HIV-1 SGA amplicon sequencing, we have developed a platform based on benchtop next-generation sequencing (NGS) (IonTorrent) accompanied by a bioinformatics pipeline capable of running on computer resources commonly available at research laboratories. During assay validation, the NGS-based sequencing of 10 HIV-1 env SGA amplicons was fully concordant with Sanger sequencing. The field test was conducted on plasma samples from 10 US Navy and Marine service members with recent HIV-1 infection (sampling interval: 2005–2010; plasma viral load: 5,884–194,984 copies/ml). The NGS analysis of 101 SGA amplicons (median: 10 amplicons/individual) showed within-individual viral sequence profiles expected in individuals at this disease stage, including individuals with highly homogeneous quasispecies, individuals with two highly homogeneous viral lineages, and individuals with heterogeneous viral populations. In a scalability assessment using the Ion Chef automated system, 41/43 tested env SGA amplicons (95%) multiplexed on a single Ion 318 chip showed consistent gene-wide coverage >50×. With lower sample requirements and higher throughput, this approach is suitable to support the increasing demand for high-quality and cost-effective HIV-1 sequences in fields such as molecular epidemiology, and development of preventive and therapeutic strategies. Keywords: Next-generation sequencing, HIV-1, Single genome amplification, Bioinformatics, IonTorrent

After more than 28,000 Ebola virus disease cases and at least 11,000 deaths in West Africa during the 2014–2016 epidemic, the world remains without a licensed vaccine or therapeutic broadly available and demonstrated to alleviate suffering. This deficiency has been felt acutely in the two, short, following years with two Ebola virus outbreaks in the Democratic Republic of Congo (DRC), and a Marburg virus outbreak in Uganda. Despite billions of U.S. dollars invested in developing medical countermeasures for filoviruses in the antecedent decades, resulting in an array of preventative, diagnostic, and therapeutic products, none are available on commercial shelves. This paper explores why just-in-time research efforts in the field during the West Africa epidemic failed, as well as some recent initiatives to prevent similarly lost opportunities.

Human immunodeficiency virus (HIV) sets several challenges for the development of a preventative HIV vaccine. Predictable, protective natural immunity against HIV does not occur and so unlike most other diseases for which vaccines exist, there are few guideposts from natural infection. Nonetheless, six vaccine efficacy trials have occurred. One in particular, the Thai trial called RV144, showed partial protective efficacy and potential ways ahead to a better vaccine approach. This coupled with other lessons from studies of acute infections as well as an increasingly complex knowledge of HIV-related vaccine immunology bring hope that a vaccine solution might be reached for this pervasive and deadly pandemic.