Comparative study of encoded and alignment-based methods for virus taxonomy classification.

The emergence of viruses and their variants has made virus taxonomy more important than ever before in controlling the spread of diseases. The creation of efficient treatments and cures that target particular virus properties can be aided by understanding virus taxonomy. Alignment-based methods are commonly used for this task, but are computationally expensive and time-consuming, especially when dealing with large datasets or when detecting new virus variants is time sensitive. An alternative approach, the encoded method, has been developed that does not require prior sequence alignment and provides faster results. However, each encoded method has its own claimed accuracy. Therefore, careful evaluation and comparison of the performance of different encoded methods are essential to identify the most accurate and reliable approach for virus taxonomy classification. This study aims to address this issue by providing a comprehensive and comparative analysis of the potential of encoded methods for virus classification and phylogenetics. We compared the vectors generated for each encoded method using distance metrics to determine their similarity to alignment-based methods. The results and their validation show that K-merNV followed by CgrDft encoded methods, perform similarly to state-of-the-art multi-sequence alignment methods. This is the first study to incorporate and compare encoded methods that will facilitate future research in making more informed decisions regarding selection of a suitable method for virus taxonomy.

Modernized Crowd Counting Strategies for Mass Gatherings-A Review.

Estimation of crowd size for large gatherings is an indispensable metric for event planners, local authorities, and emergency management. Currently, most crowd counting relies on dated methods such as people counters, entrance sensors, and ticket sales. Over the past decade, there has been rapid development in crowd counting techniques and related technology. Despite progress, theoretical advances in crowd counting technology have outpaced practical applications. The emergence of the vast array of crowd counting techniques has added to the challenge of determining those advances that can be most readily implemented. This article aims to provide an overview of promising crowd counting strategies and recent developments applied within the disaster medicine context along with the best use cases and limitations.

Current Evidence for Infection Prevention and Control Interventions in Emergency Medical Services: A Scoping Review.

OBJECTIVES: The aim of this review was to summarize current evidence from the United States on the effectiveness of practices and interventions for preventing, recognizing, and controlling occupationally acquired infectious diseases in Emergency Medical Service (EMS) clinicians. REPORT AND METHODS: PubMed, Embase, CINAHL, and SCOPUS were searched from January 1, 2006 through March 15, 2022 for studies in the United States that involved EMS clinicians and firefighters, reported on one or more workplace practices or interventions that prevented or controlled infectious diseases, and included outcome measures. Eleven (11) observational studies reported on infection prevention and control (IPC) practices providing evidence that hand hygiene, standard precautions, mandatory vaccine policies, and on-site vaccine clinics are effective. Less frequent handwashing (survey-weight adjusted odds ratio [OR] 4.20; 95% confidence interval [CI], 1.02 to 17.27) and less frequent hand hygiene after glove use (survey-weight adjusted OR 10.51; 95% CI, 2.54 to 43.45) were positively correlated with nasal colonization of Methicillin-resistant Staphylococcus aureus (MRSA). Lack of personal protective equipment (PPE) or PPE breach were correlated with higher severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seropositivity (unadjusted risk ratio [RR] 4.2; 95% CI, 1.03 to 17.22). Workers were more likely to be vaccinated against influenza if their employer offered the vaccine (unadjusted OR 3.3; 95% CI, 1.3 to 8.3). Active, targeted education modules for H1N1 influenza were effective at increasing vaccination rates and the success of on-site vaccine clinics. CONCLUSIONS: Evidence from the United States exists on the effectiveness of IPC practices in EMS clinicians, including hand hygiene, standard precautions, mandatory vaccine policies, and vaccine clinics. More research is needed on the effectiveness of PPE and vaccine acceptance.

A Scoping Review of the Essential Components of Emergency Medical Response Systems for Mass Casualty Incidents.

OBJECTIVE: Emergency medical (EM) response systems require extensive coordination, particularly during mass casualty incidents (MCIs). The recognition of preparedness gaps and contextual priorities to MCI response capacity in low- and middle-income countries (LMICs) can be better understood through the components of EM reponse systems. This study aims to delineate essential components and provide a framework for effective emergency medical response to MCIs. METHODS: A scoping review was conducted using 4 databases. Title and abstract screening was followed by full-text review. Thematic analysis was conducted to identify themes pertaining to the essential components and integration of EM response systems. RESULTS: Of 20,456 screened citations, 181 articles were included in the analysis. Seven major and 40 sub-themes emerged from the content analysis as the essential components and supportive elements of MCI medical response. The essential components of MCI response were integrated into a framework demonstrating interrelated connections between essential and supportive elements. CONCLUSIONS: Definitions of essential components of EM response to MCIs vary considerably. Most literature pertaining to MCI response originates from high income countries with far fewer reports from LMICs. Integration of essential components is needed in different geopolitical and economic contexts to ensure an effective MCI emergency medical response.

A review of infectious disease epidemiology in emergency medical service clinicians.

BACKGROUND: The emergency medical service (EMS) workforce is at high risk of occupationally-acquired infections. This review synthesized existing literature on the prevalence, incidence, and severity of infections in the EMS workforce. METHODS: We searched PubMed, Embase, CINAHL, and SCOPUS from January 1, 2006 to March 15, 2022 for studies in the US that involved EMS clinician or firefighter populations and reported 1 or more health outcomes related to occupationally-acquired infections. RESULTS: Of the 25 studies that met the inclusion criteria, most focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, with prevalence rates ranging from 1.1% to 36.2% (median 6.7%). The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in 4 studies ranged from 1.9% to 6.4%, and the prevalence of Hepatitis C in 1 study was 1.3%. Few studies reported incidence rates. The prevalence or incidence of these infections generally did not differ by age or gender, but 4 studies reported differences by race or ethnicity. In the 4 studies that compared infection rates between EMS clinicians and firefighters, EMS clinicians had a higher chance of hospitalization or death from SAR-CoV-2 (odds ratio 4.23), a higher prevalence of Hepatitis C in another study (odds ratio 1.74), and no significant difference in MRSA colonization in a separate study. CONCLUSIONS: More research is needed to better characterize the incidence and severity of occupationally-acquired infections in the EMS workforce.

Origin of novel coronavirus causing COVID-19: A computational biology study using artificial intelligence.

Origin of the COVID-19 virus (SARS-CoV-2) has been intensely debated in the scientific community since the first infected cases were detected in December 2019. The disease has caused a global pandemic, leading to deaths of thousands of people across the world and thus finding origin of this novel coronavirus is important in responding and controlling the pandemic. Recent research results suggest that bats or pangolins might be the hosts for SARS-CoV-2 based on comparative studies using its genomic sequences. This paper investigates the SARS-CoV-2 origin by using artificial intelligence (AI)-based unsupervised learning algorithms and raw genomic sequences of the virus. More than 300 genome sequences of COVID-19 infected cases collected from different countries are explored and analysed using unsupervised clustering methods. The results obtained from various AI-enabled experiments using clustering algorithms demonstrate that all examined SARS-CoV-2 genomes belong to a cluster that also contains bat and pangolin coronavirus genomes. This provides evidence strongly supporting scientific hypotheses that bats and pangolins are probable hosts for SARS-CoV-2. At the whole genome analysis level, our findings also indicate that bats are more likely the hosts for the COVID-19 virus than pangolins.

Characteristics of SARS-CoV-2 Seropositivity among Emergency Department Healthcare Workers at a Tertiary Care Center in Baltimore.

Early in the COVID-19 pandemic (March−July 2020 in Baltimore), emergency department (ED) healthcare workers (HCWs) were considered to be at greater risk of contracting SARS-CoV-2. Limited data existed, however, on the prevalence of SARS-CoV-2 infection and its impact in this workforce population. We enrolled 191 ED HCWs from a tertiary academic center, administered baseline and weekly surveys, and tested them twice (July and December 2020) for serum antibodies against SARS-CoV-2 spike protein. Approximately 6% (11 of 191, 5.8%) of ED HCWs had spike antibodies in July, a prevalence that doubled by December (21 of 174, 12.1%). A positive PCR test was self-reported by 15 of 21 (71%) seropositive and 6 of 153 (4%) seronegative HCWs (p < 0.001). Of the total 27 HCWs who had antibodies and/or were PCR positive, none required hospitalization, 18 (67%) had a self-perceived COVID-19 illness, and 12 of the 18 reported symptoms. The median number of missed workdays was 8.5 (ranging from 2 to 21). While most seropositive ED HCWs who reported symptoms took work absences, none required hospitalization, indicating that COVID-19's impact on staffing prior to vaccination was not as great as feared.

Disaster and public health emergency health data collection and management: A scoping review.

OBJECTIVE: The World Health Organization (WHO) developed the Emergency Medical Team (EMT) Minimum Data Set (MDS) to provide a structured, data-based approach to health data collection and management during disasters and public health emergencies. Given recent creation of the EMT MDS, we conducted a scoping review to gauge current practices surrounding health data collection and sharing in emergent settings. DESIGN: An English-based scoping review of PubMed and Embase databases of publications before June 28, 2021. MAIN OUTCOME MEASURES: The review aimed to identify facilitators and barriers to the implementation of the WHO-standardized health data collection systems in the context of disasters and public health emergencies; characterize best practices regarding implementation of an MDS to improve health data collection capacity in differing settings; and highlight internationally accepted, standardized tools or methods for setting up essential public health data for disaster response. RESULTS: A total of 8,038 citations from PubMed and Embase were imported into Covidence with 46 duplicates removed. Among these, 7,992 citations underwent title screening and abstract review, with 161 articles proceeding to full-text article review where an additional 109 articles were excluded. Fifty-two citations were included in final data abstraction. CONCLUSIONS: Findings revealed a range of critical operational, structural, and functional insights of relevance to implementation of the EMT MDS. The literature identified facilitators and barriers to collecting and storing disaster-based datasets, gaps in standardization of data collection resulting in poor data quality during the transition from the acute to post-acute phase, and best practices in the collection of EMT MDS.

Applications of Artificial Intelligence and Machine Learning in Disasters and Public Health Emergencies.

Indexed literature (from 2015 to 2020) on artificial intelligence (AI) technologies and machine learning algorithms (ML) pertaining to disasters and public health emergencies were reviewed. Search strategies were developed and conducted for PubMed and Compendex. Articles that met inclusion criteria were filtered iteratively by title followed by abstract review and full text review. Articles were organized to identify novel approaches and breadth of potential AI applications. A total of 1217 articles were initially retrieved by the search. Upon relevant title review, 1003 articles remained. Following abstract screening, 667 articles remained. Full text review for relevance yielded 202 articles. Articles that met inclusion criteria totaled 56 articles. Those identifying specific roles of AI and ML (17 articles) were grouped by topics highlighting utility of AI and ML in disaster and public health emergency contexts. Development and use of AI and ML have increased dramatically over the past few years. This review discusses and highlights potential contextual applications and limitations of AI and ML in disaster and public health emergency scenarios.

Developing Public Health Emergency Response Leaders in Incident Management: A Scoping Review of Educational Interventions.

During emergency responses, public health leaders frequently serve in incident management roles that differ from their routine job functions. Leaders' familiarity with incident management principles and functions can influence response outcomes. Therefore, training and exercises in incident management are often required for public health leaders. To describe existing methods of incident management training and exercises in the literature, we queried 6 English language databases and found 786 relevant articles. Five themes emerged: (1) experiential learning as an established approach to foster engaging and interactive learning environments and optimize training design; (2) technology-aided decision support tools are increasingly common for crisis decision-making; (3) integration of leadership training in the education continuum is needed for developing public health response leaders; (4) equal emphasis on competency and character is needed for developing capable and adaptable leaders; and (5) consistent evaluation methodologies and metrics are needed to assess the effectiveness of educational interventions.These findings offer important strategic and practical considerations for improving the design and delivery of educational interventions to develop public health emergency response leaders. This review and ongoing real-world events could facilitate further exploration of current practices, emerging trends, and challenges for continuous improvements in developing public health emergency response leaders.

Public Health Emergency Response Leadership Training: A Qualitative Assessment of Existing Educational Opportunities and Perceived Facilitators, Barriers, and Priorities in Professional Development.

OBJECTIVE: We aimed to understand the current training environment for developing public health emergency response leaders and highlight facilitators and barriers in accessing targeted training. DESIGN: We designed 4 focus groups to gather organizational perspectives on public health emergency response leadership development. Discussions were recorded, transcribed, coded, and analyzed to synthesize key themes. SETTING: Focus groups were convened at the 2019 Preparedness Summit (March 27-28) in St Louis, Missouri. PARTICIPANTS: Twenty-three public health professionals from 9 Public Health Emergency Preparedness (PHEP) Cooperative Agreement award recipient jurisdictions and 12 local health departments participated. MAIN OUTCOME MEASURES: We examined the current availability, relevance, specificity, and utility of educational content and delivery modalities. Facilitators and barriers were identified as opportunities to improve training access. RESULTS: Generic emergency management training is considered important and widely available but with limited application in public health practice. Existing leadership training opportunities in public health emergency response are limited and not widely known. While organizational support and accessible training facilitate participation, resource constraints (ie, funding, time, and staff) exist as key barriers. In addition, frequent staff turnover and attrition that result in loss of institutional knowledge likely hinder effective public health emergency responses. CONCLUSION: Effective public health emergency response depends on capable leaders not only well versed in specialized technical disciplines and practices but also familiar with-or preferably fluent in-emergency management principles and functions. This study demonstrated that well-aimed training strategies and organizational planning are essential in developing public health emergency response leaders. Specifically, leadership development may accrue considerable benefit from a standardized training curriculum. In addition, scalable training programs developed through public, private, and academic partnerships may lessen resource demands on individual organizations to facilitate training access. Finally, training practicums (eg, mentoring, shadowing) may provide opportunities to facilitate active learning and preserve institutional knowledge through leadership transitions.

State of public health emergency response leadership training: A multitiered organizational perspective.

OBJECTIVE: To capture organizational level information on the current state of public health emergency response leadership training. DESIGN: A web-based questionnaire. PARTICIPANTS: This multitiered assessment of health departments included two distinct respondent groups: (1) Public Health Emergency Preparedness (PHEP) Cooperative Agreement recipients (n = 34) and (2) local health departments (LHDs) (n = 169) representative of different agency sizes and populations served. RESULTS: Overall, PHEP and LHD respondents expressed a clear preference for participatory learning with practical drills/exercises and participatory workshops as the preferred training delivery modes. Compared with technical and role-specific training, leadership training was less available. For both PHEP and LHD respondents, staff availability for training is most notably limited due to lack of time. For PHEP respondents, a common factor limiting agency ability to offer training is lack of mentors/instructors, whereas for LHD respondents, it is limited funding. CONCLUSIONS: Efforts should focus on increasing accessibility and the continued development of rigorous and effective training based on practical experience in all aspects of multitiered public health emergency response leadership.

Providing Quality of Care in Fragile and Vulnerable Settings: Lessons from South Sudan.

BACKGROUND: In 2020, the World Health Organization (WHO) released a report concerning planning and actions to provide quality of care in fragile, conflict-affected, and vulnerable areas. South Sudan, the world's newest country, has encountered both natural and man-made disasters in recent years that have posed marked challenges to delivery of care. The Southern Sudan Healthcare Organization (SSHCO) operates as a non-governmental organization (NGO) in this setting, delivering and improving healthcare through war, flooding, and infectious outbreaks. OBJECTIVE: The goal of this paper is to highlight the challenges faced in providing care in South Sudan from an NGO perspective and apply the recent WHO guidelines on quality of care to optimize practical implementation. METHOD: Each of the WHO's eight elements for quality of care in South Sudan were examined in relation to the experience of SSHCO from 2013-2021. Analysis included: 1. summary of the WHO element; 2. examples of successful implementation; 3. barriers to implementation; and 4. recommendations to improve implementation. FINDINGS: The team found that communication and coordination were the most important aspects of improving quality of care in South Sudan. These should be prioritized and include intergovernmental partners, the local and national Ministry of Health (MOH), NGOs, and community stakeholders. Communication and coordination should foster community engagement, improved data collecting and reporting, and sharing of publicly accessible information. Better clinical staff training and governance are also required to ensure the most effective use of limited resources. CONCLUSION: South Sudan faces many barriers to quality of care with communication and coordination identified among the foremost issues. Practical application of the WHO elements of quality of care can assist NGOs in effectively identifying areas for improvement to deliver better quality essential health services.

Perspectives on xenophobia during epidemics and implications for emergency management.

Coronavirus disease 2019 (COVID-19) is an infectious disease that traces its earliest known cases to the Hubei region of China in late 2019. As the COVID-19 pandemic has spread across the globe wreaking unprecedented disruption, increasing levels of xenophobia and racial discrimination have been documented against those of Asian descent. We investigate the historical connections between disease and rise of xenophobia as described in the peer-reviewed literature addressing prior epidemics, such as Ebola and the Hong Kong Flu, in conjunction with concurrent cases of prejudice toward certain groups of people. Attempts to better understand why such attitudes emerge are examined in the context of xenophobic actions during pandemics. Prevailing views suggest that xenophobia ultimately leads to increased stigmatization of those afflicted by disease, which in turn leads to decreased trust in the medical system, resulting in a negative feedback loop. Accurate disseminated information and improved public education on sources and modes of transmission of infectious diseases are essential to check xenophobic tendencies, reduce negative effects and foster greater cooperation.

Pandemic influenza and major disease outbreak preparedness in US emergency departments: A selected survey of emergency health professionals.

OBJECTIVE: To assess the level of pandemic preparedness at emergency departments (EDs) around the country and to better understand current barriers to preparedness in the United States represented by health professionals in the American College of Emergency Physician (ACEP) Disaster Medicine Section (DMS). Methods, design, and setting: A cross-sectional survey of ACEP DMS members was performed. A total of 300 members were surveyed both via e-mail and with paper surveys during the 2009 ACEP Scientific Assembly DMS Meeting. An optional comments section was included for section members' perspectives on barriers to preparedness. A 15-item pandemic preparedness score was calculated for each respondent based on key preparedness indicators as defined by the authors. Results were analyzed with descriptive statistics, χ2 analysis, Cochran-Armitage trend test, and analysis of variance. Free text comments were coded and subjected to frequency-based analysis. RESULTS: A total of 92 DMS members completed the survey with a response rate of 31 percent. Although 85 percent of those surveyed indicated that their hospital had a plan for pandemic influenza response and other infectious disease threats, only 68 percent indicated that their ED had a plan, and 52 percent indicated that their hospital or ED had conducted disaster preparedness drills. Only 57 percent indicated that there was a plan to augment ED staff in the event of a staffing shortage, and 63 percent indicated that there were adequate supplies of personal protective equipment. While 63 percent of respondents indicated that their ED had a plan for distribution of vaccines and antivirals, only 32 percent of EDs had a plan for allocation of ventilators. A total of 42 percent of respondents felt that their ED was prepared in the event of a pandemic influenza or other disease outbreak, and only 35 percent felt that their hospital was prepared. The average pandemic preparedness score among respondents was 8.30 of a total of 15. Larger EDs were more likely to have a higher preparedness score (p = 0.03) and more likely to have a pandemic preparedness plan (p = 0.037). Some major barriers to preparedness cited by section members included lack of local administration support, challenges in funding, need for dedicated disaster preparedness personnel, staffing shortages, and a lack of communication among disaster response agencies, particularly at the federal level. CONCLUSIONS: There appear to be significant gaps in pandemic influenza and other infectious disease outbreak planning among the hospitals where ACEP DMS members work. This may reflect a broader underlying inadequacy of preparedness measures.

Fire at the Oakland Ghost Ship Warehouse: A disaster life cycle-based analysis.

OBJECTIVE: Structural fires remain a prominent threat to public health and safety even in several regions of the developed world, where rising housing costs force many to reside in unsafe environments. This case report of the Ghost Ship Warehouse fire in Oakland, California, highlights deficiencies in the emergency management system in the context of similar nightclub incidents to inform recommendations that might prevent such events from occurring in the future. DESIGN: The characteristics of the Ghost Ship warehouse and circumstances surrounding the fire, as described in government documents and news media sources, were examined using the disaster life cycle framework. The Ghost Ship fire was also compared with two prior fire disasters at the Happy Land nightclub in New York City and Station nightclub in West Warwick, Rhode Island. RESULTS: The following risk factors were identified as common features of deadly nightclub fires: large crowd size, limited access to exits, multiple code violations, lack of required permits, inadequate fire suppression systems, and poor building maintenance. CONCLUSIONS: To prevent the recurrence of such disasters, Oakland and other cities should adopt measures to improve interdepartmental communication; streamline reporting of fire and safety hazards, and allocate sufficient resources and staff capable of identifying hazardous buildings, performing inspections, and enforcing building and fire codes. Equally importantly, the urban affordable housing crisis needs to be adequately addressed to mitigate vulnerable populations living in unsafe dwellings that place them at risk of deadly fires.

Pilgrim Satisfaction in a Mass Religious Gathering: Study from Sabarimala Destination, Kerala State of India.

Identification of basic factors of pilgrim satisfaction is essential to responsive authorities for effective implementation of devotee welfare programmes. The determinants of satisfaction in a particular location are comprised of environmental, economic and sociocultural activities. The Sabarimala hill temple is one of the major Sastha temples in India. Every year, about 25 million pilgrims visit the temple from all parts of the country and abroad. The present study analyzes devotee satisfaction according to their demographic profile and identifies key factors that affect the overall satisfaction of pilgrims visiting the temple at the Sabarimala mass gathering destination. A total of 526 visitors were contacted with a prestructured, field tested questionnaire. This was analyzed using the Statistical Package for Social Sciences. Factor analysis, regression analysis and two-step cluster analysis were used to elucidate satisfaction parameters. The identified factor groupings for pilgrim satisfaction at Sabarimala destination are food and accommodation, safety and security, health and sanitation, ecology and environment and and communication and transportation. From the analysis of various results of the present study, it is evident that the mass pilgrimage of Sabarimala destination exhibits the signs of a secular experience and its visitors are mainly motivated by spiritual aspects.

Using mind mapping technology for personal preparedness planning.

OBJECTIVE: Organizing key information for personal disaster preparedness in an efficient and accessible format is critical to ensure practical utility. The authors examine the use of mind mapping technology to organize personal disaster preparedness information and explore the potential of mind mapping software as a tool to create individual and family preparedness resources. DESIGN: The general features of mind maps are considered and a sample family preparedness plan was created using TheBrain, a mind mapping software. RESULTS: Mind maps are a promising tool to organize personal preparedness plans with the ability to include significant amounts of varied information in a structure that emphasizes relationships between topics and enables collaborative sharing.

Push-to-talk apps for disaster communications: Hurricane season brings technology adaptation.

Effective communication during disasters is essential for emergency management, responders, and impacted populations. Recent hurricanes have drawn attention to the potential utility of push-to-talk (PTT) applications with some such as Zello, garnering over 6 million downloads during the week prior to Hurricane Irma. PTT technology integrates a two-way radio system to transmit and receive messages via point-to-point communication lines. With rapid implementation of newer technology and applications often driven by anecdotal reports and the media, the actual performance impact of such technology in the face of disasters is challenging to assess. This article attempts to characterize advantages and limitations of PTT in the context of hurricanes through primary news article sources.