Environment, vector, or host? Using machine learning to untangle the mechanisms driving arbovirus outbreaks.

Climatic, landscape, and host features are critical components in shaping outbreaks of vector-borne diseases. However, the relationship between the outbreaks of vector-borne pathogens and their environmental drivers is typically complicated, nonlinear, and may vary by taxonomic units below the species level (e.g., strain or serotype). Here, we aim to untangle how these complex forces shape the risk of outbreaks of Bluetongue virus (BTV); a vector-borne pathogen that is continuously emerging and re-emerging across Europe, with severe economic implications. We tested if the ecological predictors of BTV outbreak risk were serotype-specific by examining the most prevalent serotypes recorded in Europe (1, 4, and 8). We used a robust machine learning (ML) pipeline and 23 relevant environmental features to fit predictive models to 24,245 outbreaks reported in 25 European countries between 2000 and 2019. Our ML models demonstrated high predictive performance for all BTV serotypes (accuracies > 0.87) and revealed strong nonlinear relationships between BTV outbreak risk and environmental and host features. Serotype-specific analysis suggests, however, that each of the major serotypes (1, 4, and 8) had a unique outbreak risk profile. For example, temperature and midge abundance were as the most important characteristics shaping serotype 1, whereas for serotype 4 goat density and temperature were more important. We were also able to identify strong interactive effects between environmental and host characteristics that were also serotype specific. Our ML pipeline was able to reveal more in-depth insights into the complex epidemiology of BTVs and can guide policymakers in intervention strategies to help reduce the economic implications and social cost of this important pathogen.

Phylogeographical and cross-species transmission dynamics of SAT1 and SAT2 foot-and-mouth disease virus in Eastern Africa.

Understanding the dynamics of foot-and-mouth disease virus (FMDV), an endemic and economically constraining disease, is critical in designing control programmes in Africa. This study investigates the evolutionary epidemiology of SAT1 and SAT2 FMDV in Eastern Africa, as well as between cattle and wild African buffalo. Bayesian phylodynamic models were used to analyse SAT1 and SAT2 VP1 gene segments collected between 1975 and 2016, focusing on the SAT1 and SAT2 viruses currently circulating in Eastern Africa. The root state posterior probabilities inferred from our analyses suggest Zimbabwe as the ancestral location for SAT1 currently circulating in Eastern Africa (p = 0.67). For the SAT2 clade, Kenya is inferred to be the ancestral location for introduction of the virus into other countries in Eastern Africa (p = 0.72). Salient (Bayes factor >10) viral dispersal routes were inferred from Tanzania to Kenya, and from Kenya to Uganda for SAT1 and SAT2, respectively. Results suggest that cattle are the source of the SAT1 and SAT2 clades currently circulating in Eastern Africa. In addition, our results suggest that the majority of SAT1 and SAT2 in livestock come from other livestock rather than wildlife, with limited evidence that buffalo serve as reservoirs for cattle. Insights from the present study highlight the role of cattle movements and anthropogenic activities in shaping the evolutionary history of SAT1 and SAT2 in Eastern Africa. While the results may be affected by inherent limitations of imperfect surveillance, our analysis elucidates the dynamics between host species in this region, which is key to guiding disease intervention activities.

Complete Genome Sequencing of Influenza A Viruses within Swine Farrow-to-Wean Farms Reveals the Emergence, Persistence, and Subsidence of Diverse Viral Genotypes.

Influenza A viruses (IAVs) are endemic in swine and represent a public health risk. However, there is limited information on the genetic diversity of swine IAVs within farrow-to-wean farms, which is where most pigs are born. In this longitudinal study, we sampled 5 farrow-to-wean farms for a year and collected 4,190 individual nasal swabs from three distinct pig subpopulations. Of these, 207 (4.9%) samples tested PCR positive for IAV, and 124 IAVs were isolated. We sequenced the complete genomes of 123 IAV isolates and found 31 H1N1, 26 H1N2, 63 H3N2, and 3 mixed IAVs. Based on the IAV hemagglutinin, seven different influenza A viral groups (VGs) were identified. Most of the remaining IAV gene segments allowed us to differentiate the same VGs, although an additional viral group was identified for gene segment 3 (PA). Moreover, the codetection of more than one IAV VG was documented at different levels (farm, subpopulation, and individual pigs), highlighting the environment for potential IAV reassortment. Additionally, 3 out of 5 farms contained IAV isolates (n = 5) with gene segments from more than one VG, and 79% of all the IAVs sequenced contained a signature mutation (S31N) in the matrix gene that has been associated with resistance to the antiviral amantadine. Within farms, some IAVs were detected only once, while others were detected for 283 days. Our results illustrate the maintenance and subsidence of different IAVs within swine farrow-to-wean farms over time, demonstrating that pig subpopulation dynamics are important to better understand the diversity and epidemiology of swine IAVs.IMPORTANCE On a global scale, swine are one of the main reservoir species for influenza A viruses (IAVs) and play a key role in the transmission of IAVs between species. Additionally, the 2009 IAV pandemics highlighted the role of pigs in the emergence of IAVs with pandemic potential. However, limited information is available regarding the diversity and distribution of swine IAVs on farrow-to-wean farms, where novel IAVs can emerge. In this study, we studied 5 swine farrow-to-wean farms for a year and characterized the genetic diversity of IAVs among three different pig subpopulations commonly housed on this type of farm. Using next-generation-sequencing technologies, we demonstrated the complex distribution and diversity of IAVs among the pig subpopulations studied. Our results demonstrated the dynamic evolution of IAVs within farrow-to-wean farms, which is crucial to improve health interventions to reduce the risk of transmission between pigs and from pigs to people.

Genetic characterization of spotted fever group rickettsiae in questing ixodid ticks collected in Israel and environmental risk factors for their infection.

This study aimed to genetically characterize spotted fever group rickettsiae (SFGR) in questing ixodid ticks from Israel and to identify risk factors associated with SFGR-positive ticks using molecular techniques and geographic information systems (GIS) analysis. 1039 ticks from the genus Rhipicephalus were collected during 2014. 109/1039 (10·49%) carried SFGR-DNA of either Rickettsia massiliae (95), 'Candidatus Rickettsia barbariae' (8) or Rickettsia conorii (6). Higher prevalence of SFGR was found in Rhipicephalus turanicus (18·00%) compared with Rhipicephalus sanguineus sensu lato (3·22%). Rickettsia massiliae was the most commonly detected species and the most widely disseminated throughout Israel (87·15% of all Rickettsia-positive ticks). GIS analysis revealed that Central and Northern coastal regions are at high risk for SFGR. The presence of ticks was significantly associated with normalized difference vegetation index and temperature variation over the course of the year. The presence of rickettsiae was significantly associated with brown type soils, higher land surface temperature and higher precipitation. The latter parameters may contribute to infection of the tick with SFGR. Health care professionals should be aware of the possible exposure of local communities and travellers to R. massillae. Molecular and geographical information can help professionals to identify areas that are susceptible to SFGR-infected ticks.

Interpretable machine learning models for predicting in-hospital and 30 days adverse events in acute coronary syndrome patients in Kuwait.

The relationships between acute coronary syndromes (ACS) adverse events and the associated risk factors are typically complicated and nonlinear, which poses significant challenges to clinicians' attempts at risk stratification. Here, we aim to explore the implementation of modern risk stratification tools to untangle how these complex factors shape the risk of adverse events in patients with ACS. We used an interpretable multi-algorithm machine learning (ML) approach and clinical features to fit predictive models to 1,976 patients with ACS in Kuwait. We demonstrated that random forest (RF) and extreme gradient boosting (XGB) algorithms, remarkably outperform traditional logistic regression model (AUCs = 0.84 & 0.79 for RF and XGB, respectively). Our in-hospital adverse events model identified left ventricular ejection fraction as the most important predictor with the highest interaction strength with other factors. However, using the 30-days adverse events model, we found that performing an urgent coronary artery bypass graft was the most important predictor, with creatinine levels having the strongest overall interaction with other related factors. Our ML models not only untangled the non-linear relationships that shape the clinical epidemiology of ACS adverse events but also elucidated their risk in individual patients based on their unique features.

Anxiety disorders among children and adolescents during COVID-19 lockdowns and school closures: a cross-sectional study in Kuwait.

Introduction: Investigating the epidemiology of mental health disorders resulting from COVID-19 intervention measures, primary school closures, and social isolation in children and adolescents needs to be prioritized over adults at the post-pandemic stage. Most preliminary psychosocial studies conducted during the pandemic have demonstrated that younger age groups are the most vulnerable to such implications. Thus, this study aims to estimate the probable prevalence of specific anxiety disorders in children and quantify their relationships with relevant demographic risk factors. Methods: We used a cross-sectional study comprising 430 children aged between 8- and 18 years old living in Kuwait during the period of school closures as well as full and partial lockdowns. The survey included questions about participants' characteristics, children's anxiety using the Screen for Child Anxiety Related Emotional Disorders Questionnaire (SCARED) scale, and children's emotions and behaviours using the Strengths and Difficulties Questionnaire (SDQ). Univariate and multivariate logistic regression analyses were used to summarize the demographic and characteristics of the participants and their association with general, social, and generalized anxieties, as well as behavioural and emotional difficulties. Results: We inferred that 24.83% of our participants had at least one anxiety disorder, while 20.19% were classified as abnormal on the SDQ scale. Our multivariate analysis revealed that lockdown duration and sex of the child were consistently significant predictors (p-values < 0.05) of the broad spectrum of selected mental disorders. Additionally, we inferred notable increases in the likelihood of mental disorders associated with the increased duration of lockdowns. Conclusions: Our findings revealed preliminary insights into the vulnerability of young populations to the indirect negative impacts of strict public health measures during pandemic emergencies. Thus, authorities should consider such implications when planning and implementing similar interventions in future pandemics.

Psychiatrists' Insights on Integrating Occupational Therapy in Mental Health Care: A Multisite Middle Eastern Study.

Objective: The purpose of this study was to explore the knowledge, perception, attitude, and self-efficacy of psychiatrists regarding the role of occupational therapy in mental health practice. Materials and Methods: This study utilized a cross-sectional design to examine the perspectives of psychiatrists from various Middle Eastern countries on occupational therapy practice. A self-developed tool was mainly used to assess occupational therapy knowledge, autonomy, attitude, and self-efficacy. STATA version 16.0 was employed for all subsequent statistical analyses. The data were analyzed using the Kruskal-Wallis and chi-square tests. Results: A total of 117 participants (psychiatrists) from various Middle Eastern countries, including Kuwait, Bahrain, Saudi Arabia, and Jordan, took part in this study. Overall, no significant differences were found between the sites in terms of knowledge and self-perception of occupational therapy autonomy, indicating a lack of understanding about the unique nature of occupational therapy as a distinct health care profession (p-values > 0.05). However, this study's participants demonstrated a positive attitude and self-efficacy towards occupational therapy. Conclusions: In order to promote the desired therapeutic outcomes, a referral form for occupational therapy, encompassing the main areas of intervention, was proposed. Such a referral form can help inform psychiatrists about the key components of occupational therapy services in mental health practice, thus facilitating the desired interprofessional collaboration and patient outcomes. This study's implications and future directions are also discussed.

Psychological Disorders and Coping among Undergraduate College Students: Advocating for Students' Counselling Services at Kuwait University.

Objectives: The objectives of the current study are twofold. First, it aimed to explore the prevalence of depression, anxiety and stress symptoms (i.e., psychological disorders) among Kuwait University students. Second, it sought to identify and quantify the associated risk factors as well as the students' coping strategies utilized to address these psychological disorders. Methods: We used a cross-sectional study at Kuwait University and selected students using a multistage stratified cluster sampling design among the 15 faculties of Kuwait University. To serve the study purposes, two cross-cultural and validated instruments were used, including the Depression, Anxiety and Stress Scale 21 (DASS-21) and the Brief-COPE scale. Descriptive statistics, as well as logistic regression analysis, were used to analyze the study findings. Results: A sample of 1142 students from various faculties participated in this study. We found that 681 (59.6%), 791 (69.3%) and 588 (51.5%) of the participants had depression, anxiety and stress symptoms, respectively. The highest coping strategies for stressors and challenges faced were moderate and high emotion-based coping strategies (n = 1063, 93.1%). Students from the Faculty of Allied Health Sciences as well as students from the Faculty of Engineering had significantly higher stress levels compared with students from other faculties (p < 0.05). Our results demonstrated that family problems were consistently a significant predictor of depression, anxiety and stress symptoms among Kuwait University students (p < 0.05). We further found that students who presented with stress and anxiety symptoms and those who practiced avoidant-focused coping strategies were substantially more likely to experience depression (ORs ≥ 2.7, p < 0.01). Conclusions: Our findings inferred that the majority of Kuwait University students have a remarkably high prevalence of mental health problems, mainly anxiety, depression, and stress symptoms along with inconsistent coping strategies toward the faced challenges during their studies. Therefore, the most important recommendation of the current study is the establishment of counselling centers in all faculties at Kuwait University. In turn, doing so facilitates the integration of wellness programs and the provision of comprehensive educational seminars, specialized training sessions and self-management techniques for Kuwait University students, leading to desired academic outcomes.

Anemia or other comorbidities? using machine learning to reveal deeper insights into the drivers of acute coronary syndromes in hospital admitted patients.

Acute coronary syndromes (ACS) are a leading cause of deaths worldwide, yet the diagnosis and treatment of this group of diseases represent a significant challenge for clinicians. The epidemiology of ACS is extremely complex and the relationship between ACS and patient risk factors is typically non-linear and highly variable across patient lifespan. Here, we aim to uncover deeper insights into the factors that shape ACS outcomes in hospitals across four Arabian Gulf countries. Further, because anemia is one of the most observed comorbidities, we explored its role in the prognosis of most prevalent ACS in-hospital outcomes (mortality, heart failure, and bleeding) in the region. We used a robust multi-algorithm interpretable machine learning (ML) pipeline, and 20 relevant risk factors to fit predictive models to 4,044 patients presenting with ACS between 2012 and 2013. We found that in-hospital heart failure followed by anemia was the most important predictor of mortality. However, anemia was the first most important predictor for both in-hospital heart failure, and bleeding. For all in-hospital outcome, anemia had remarkably non-linear relationships with both ACS outcomes and patients' baseline characteristics. With minimal statistical assumptions, our ML models had reasonable predictive performance (AUCs > 0.75) and substantially outperformed commonly used statistical and risk stratification methods. Moreover, our pipeline was able to elucidate ACS risk of individual patients based on their unique risk factors. Fully interpretable ML approaches are rarely used in clinical settings, particularly in the Middle East, but have the potential to improve clinicians' prognostic efforts and guide policymakers in reducing the health and economic burdens of ACS worldwide.

Comparative phylodynamics reveals the evolutionary history of SARS-CoV-2 emerging variants in the Arabian Peninsula.

Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to be responsible for an unprecedented worldwide public health and economic catastrophe. Accurate understanding and comparison of global and regional evolutionary epidemiology of novel SARS-CoV-2 variants are critical to guide current and future interventions. Here, we utilized a Bayesian phylodynamic pipeline to trace and compare the evolutionary dynamics, spatiotemporal origins, and spread of five variants (Alpha, Beta, Delta, Kappa, and Eta) across the Arabian Peninsula. We found variant-specific signatures of evolution and spread that are likely linked to air travel and disease control interventions in the region. Alpha, Beta, and Delta variants went through sequential periods of growth and decline, whereas we inferred inconclusive population growth patterns for the Kappa and Eta variants due to their sporadic introductions in the region. Non-pharmaceutical interventions imposed between mid-2020 and early 2021 likely played a role in reducing the epidemic progression of the Beta and the Alpha variants. In comparison, the combination of the non-pharmaceutical interventions and the rapid rollout of vaccination might have shaped Delta variant dynamics. We found that the Alpha and Beta variants were frequently introduced into the Arab peninsula between mid-2020 and early 2021 from Europe and Africa, respectively, whereas the Delta variant was frequently introduced between early 2021 and mid-2021 from East Asia. For these three variants, we also revealed significant and intense dispersal routes between the Arab region and Africa, Europe, Asia, and Oceania. In contrast, the restricted spread and stable effective population size of the Kappa and the Eta variants suggest that they no longer need to be targeted in genomic surveillance activities in the region. In contrast, the evolutionary characteristics of the Alpha, Beta, and Delta variants confirm the dominance of these variants in the recent outbreaks. Our study highlights the urgent need to establish regional molecular surveillance programs to ensure effective decision making related to the allocation of intervention activities targeted toward the most relevant variants.

Predictors of intensive care unit admission and mortality in SARS-CoV-2 infection: A cross sectional study at a tertiary care hospital.

Background: The transmissibility and associated morbidity and mortality of severe acute respiratory syndrome-related coronavirus (SARS-Cov-2), have overwhelmed worldwide healthcare systems, resulting in an urgent need to understand this virus and its associated effects. The aim of our study was to identify patient symptoms, clinical characteristics, laboratory, and radiology findings that are associated with serious morbidity and mortality in COVID-19 patients. Methods: A cross sectional study was conducted in Jaber Al Ahmad Hospital, the designated COVID-19 center in Kuwait between August 1st, 2020 and January 31st, 2021. The main outcomes measured in this study were to identify variables associated with intensive care unit (ICU) admission, as proxy for serious morbidity, and in hospital mortality. Results: Two hundred and seventy-six patients were included in the study. Thirty-six (13%) patients were admitted to intensive care unit (ICU) and 33 (12%) patients expired. On multivariate analysis we found having elevated fibrinogen [OR 1.39, 95% CI 1.08-1.64, P = 0.04], low estimated glomerular filtration rate (eGFR) [OR 0.89, 95% CI 0.81-0.95, P = 0.02], and having bilateral patchy lung shadowing [OR 6.68, 95% CI 1.85-15.28, P < 0.01] to be significantly associated with increase odds of ICU admission. Elevated CRP [OR 1.25, 95% CI 1.10-1.98, P < 0.01], low eGFR [OR 0.95, 95% CI 0.90-0.99, P = 0.05] and having ischemic heart disease [OR 7.03, 95% CI 1.60-46.42, P = 0.04] were independently associated with increased odds of mortality. Conclusion: Certain inflammatory and coagulopathy markers, and having certain lung radiological features, in addition to having medical comorbidities, specifically, ischemic heart disease and renal impairment are key predictors for serious morbidity and mortality in patients infected with COVID-19. These should be incorporated into medical institutes risk assessment tools used by physicians and policy makers to instigate, prioritize, and reprioritize care in patients with COVID-19 and instigate preventative strategy to reduce the impact of future outbreak.

Integrating animal movements with phylogeography to model the spread of PRRSV in the USA.

Viral sequence data coupled with phylodynamic models have become instrumental in investigating the outbreaks of human and animal diseases, and the incorporation of the hypothesized drivers of pathogen spread can enhance the interpretation from phylodynamic inference. Integrating animal movement data with phylodynamics allows us to quantify the extent to which the spatial diffusion of a pathogen is influenced by animal movements and contrast the relative importance of different types of movements in shaping pathogen distribution. We combine animal movement, spatial, and environmental data in a Bayesian phylodynamic framework to explain the spatial diffusion and evolutionary trends of a rapidly spreading sub-lineage (denoted L1A) of porcine reproductive and respiratory syndrome virus (PRRSV) Type 2 from 2014 to 2017. PRRSV is the most important endemic pathogen affecting pigs in the USA, and this particular virulent sub-lineage emerged in 2014 and continues to be the dominant lineage in the US swine industry to date. Data included 984 open reading frame 5 (ORF5) PRRSV L1A sequences obtained from two production systems in a swine-dense production region (∼85,000 mi2) in the USA between 2014 and 2017. The study area was divided into sectors for which model covariates were summarized, and animal movement data between each sector were summarized by age class (wean: 3-4 weeks; feeder: 8-25 weeks; breeding: ≥21 weeks). We implemented a discrete-space phylogeographic generalized linear model using Bayesian evolutionary analysis by sampling trees (BEAST) to infer factors associated with variability in between-sector diffusion rates of PRRSV L1A. We found that between-sector spread was enhanced by the movement of feeder pigs, spatial adjacency of sectors, and farm density in the destination sector. The PRRSV L1A strain was introduced in the study area in early 2013, and genetic diversity and effective population size peaked in 2015 before fluctuating seasonally (peaking during the summer months). Our study underscores the importance of animal movements and shows, for the first time, that the movement of feeder pigs (8-25 weeks old) shaped the spatial patterns of PRRSV spread much more strongly than the movements of other age classes of pigs. The inclusion of movement data into phylodynamic models as done in this analysis may enhance our ability to identify crucial pathways of disease spread that can be targeted to mitigate the spatial spread of infectious human and animal pathogens.

Prevalence, predictors and outcomes of bleeding events in patients with COVID-19 infection on anticoagulation: Retrospective cohort study.

BACKGROUND: This study aims to examine risk factors and complications associated with bleeding events in patients with COVID-19 who are on anticoagulation. MATERIAL AND METHODS: We conducted retrospective review of all patients who were admitted with COVID-19 and developed bleeding events between March and June 2020. Data were analyzed in accordance with three major outcomes. Mortality within 30 days of bleeding episode, resolution of the bleeding event, and the type of bleeding event. RESULTS: Of 122 bleeds, there was 55 (28 %) gastrointestinal (GI) bleeds. Overall mortality was 59 % (n = 72). The prevalence of therapeutic invasive interventions was 11.5 % (n = 14) all were successful in resolving the bleeding event. We found that having a GI bleeds was associated with higher risk of mortality compared to non-GI bleeds (p = 0.04) and having occult bleeds to be associated with 15 times increased risk of mortality (OR 15, 95%CI 1.97-29.1, p = 0.01). Furthermore, patients who were on no anticoagulation (none) (OR 0.1, 95%CI 0.01-0.86, p < 0.00), on prophylactic dose anticoagulation (OR 0.07, 95%CI 0.02-0.28, p = 0.03) or intermediate dose anticoagulation (OR 0.36, 95%CI 0.09-1.34, p = 0.13) were less likely to die than patients on therapeutic dose. CONCLUSIONS: The best approach to manage COVID-19 bleeding patients is to prioritize therapies that manage sepsis induce coagulopathy and shock over other approaches. In COVID-19 patients' routine prescription of supra-prophylactic dose anticoagulation should be revisited and more individualized approach to prescription should be the norm. Regardless of the cause of bleeding event it appears that the majority of bleeding events resolve with noninvasive interventions and when invasive interventions were necessary, they were associated with high success rate despite the delay.

Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza Outbreaks.

Emerging and endemic animal viral diseases continue to impose substantial impacts on animal and human health. Most current and past molecular surveillance studies of animal diseases investigated spatio-temporal and evolutionary dynamics of the viruses in a disjointed analytical framework, ignoring many uncertainties and made joint conclusions from both analytical approaches. Phylodynamic methods offer a uniquely integrated platform capable of inferring complex epidemiological and evolutionary processes from the phylogeny of viruses in populations using a single Bayesian statistical framework. In this study, we reviewed and outlined basic concepts and aspects of phylodynamic methods and attempted to summarize essential components of the methodology in one analytical pipeline to facilitate the proper use of the methods by animal health researchers. Also, we challenged the robustness of the posterior evolutionary parameters, inferred by the commonly used phylodynamic models, using hemagglutinin (HA) and polymerase basic 2 (PB2) segments of the currently circulating human-like H3 swine influenza (SI) viruses isolated in the United States and multiple priors. Subsequently, we compared similarities and differences between the posterior parameters inferred from sequence data using multiple phylodynamic models. Our suggested phylodynamic approach attempts to reduce the impact of its inherent limitations to offer less biased and biologically plausible inferences about the pathogen evolutionary characteristics to properly guide intervention activities. We also pinpointed requirements and challenges for integrating phylodynamic methods in routine animal disease surveillance activities.

Global emergence and evolutionary dynamics of bluetongue virus.

Bluetongue virus (BTV) epidemics are responsible for worldwide economic losses of up to US$ 3 billion. Understanding the global evolutionary epidemiology of BTV is critical in designing intervention programs. Here we employed phylodynamic models to quantify the evolutionary characteristics, spatiotemporal origins, and multi-host transmission dynamics of BTV across the globe. We inferred that goats are the ancestral hosts for BTV but are less likely to be important for cross-species transmission, sheep and cattle continue to be important for the transmission and maintenance of infection between other species. Our models pointed to China and India, countries with the highest population of goats, as the likely ancestral country for BTV emergence and dispersal worldwide over 1000 years ago. However, the increased diversification and dispersal of BTV coincided with the initiation of transcontinental livestock trade after the 1850s. Our analysis uncovered important epidemiological aspects of BTV that may guide future molecular surveillance of BTV.

Spatiotemporal dynamics of the COVID-19 pandemic in the State of Kuwait.

OBJECTIVES: Prompt understanding of the temporal and spatial patterns of the COVID-19 pandemic on a national level is a critical step for the timely allocation of surveillance resources. Therefore, this study explored the temporal and spatiotemporal dynamics of the COVID-19 pandemic in Kuwait using daily confirmed case data collected between the 23 February and 07 May 2020. METHODS: The pandemic progression was quantified using the time-dependent reproductive number (R(t)). The spatiotemporal scan statistic model was used to identify local clustering events. Variability in transmission dynamics was accounted for within and between two socioeconomic classes: citizens-residents and migrant workers. RESULTS: The pandemic size in Kuwait continues to grow (R(t)s ≥2), indicating significant ongoing spread. Significant spreading and clustering events were detected among migrant workers, due to their densely populated areas and poor living conditions. However, the government's aggressive intervention measures have substantially lowered pandemic growth in migrant worker areas. However, at a later stage of the study period, active spreading and clustering events among both socioeconomic classes were found. CONCLUSIONS: This study provided deeper insights into the epidemiology of COVID-19 in Kuwait and provided an important platform for rapid guidance of decisions related to intervention activities.

Phylodynamics and evolutionary epidemiology of African swine fever p72-CVR genes in Eurasia and Africa.

African swine fever (ASF) is a complex infectious disease of swine that constitutes devastating impacts on animal health and the world economy. Here, we investigated the evolutionary epidemiology of ASF virus (ASFV) in Eurasia and Africa using the concatenated gene sequences of the viral protein 72 and the central variable region of isolates collected between 1960 and 2015. We used Bayesian phylodynamic models to reconstruct the evolutionary history of the virus, to identify virus population demographics and to quantify dispersal patterns between host species. Results suggest that ASFV exhibited a significantly high evolutionary rate and population growth through time since its divergence in the 18th century from East Africa, with no signs of decline till recent years. This increase corresponds to the growing pig trade activities between continents during the 19th century, and may be attributed to an evolutionary drift that resulted from either continuous circulation or maintenance of the virus within Africa and Eurasia. Furthermore, results implicate wild suids as the ancestral host species (root state posterior probability = 0.87) for ASFV in the early 1700s in Africa. Moreover, results indicate the transmission cycle between wild suids and pigs is an important cycle for ASFV spread and maintenance in pig populations, while ticks are an important natural reservoir that can facilitate ASFV spread and maintenance in wild swine populations. We illustrated the prospects of phylodynamic methods in improving risk-based surveillance, support of effective animal health policies, and epidemic preparedness in countries at high risk of ASFV incursion.

Surveillance of porcine reproductive and respiratory syndrome virus in the United States using risk mapping and species distribution modeling.

Porcine reproductive and respiratory syndrome virus (PRRSv) outbreaks cause significant financial losses to the U.S. swine industry, where the pathogen is endemic. Seasonal increases in the number of outbreaks are typically observed using PRRSv epidemic curves. However, the nature and extent to which demographic and environmental factors influence the risk for PRRSv outbreaks in the country remains unclear. The objective of this study was to develop risk maps for PRRSv outbreaks across the United States (U.S.) and compare ecological dynamics of the disease in five of the most important swine production regions of the country. This study integrates spatial information regarding PRRSv surveillance with relevant demographic and environmental factors collected between 2009 and 2016. We used presence-only Maximum Entropy (Maxent), a species distribution modeling approach, to model the spatial risk of PRRSv in swine populations. Data fitted the selected model relatively well when the modeling approach was conducted by region (training and testing AUCs<0.75). All of the Maxent models selected identified high-risk areas, with probabilities greater than 0.5. The relative contribution of pig density to PRRSv risk was highest in pig-densely populated areas (Minnesota, Iowa and North Carolina), whereas climate and land cover were important in areas with relatively low pig densities (Illinois, Indiana, South Dakota, Nebraska, Kansas, Oklahoma, Colorado, and Texas). Although many previous studies associated the risk of PRRSv with high pig density and climatic factors, the study here quantifies, for the first time in the peer-reviewed literature, the spatial variation and relative contribution of these factors across different swine production regions in the U.S. The results will help in the design and implement of early detection, prevention, and control strategies for one of the most devastating diseases affecting the swine industry in the U.S.

Novel approaches for Spatial and Molecular Surveillance of Porcine Reproductive and Respiratory Syndrome Virus (PRRSv) in the United States.

The US swine industry has been impaired over the last 25 years by the far-reaching financial losses caused by the porcine reproductive and respiratory syndrome (PRRS). Here, we explored the relations between the spatial risk of PRRS outbreaks and its phylodynamic history in the U.S during 1998-2016 using ORF5 sequences collected from swine farms in the Midwest region. We used maximum entropy and Bayesian phylodynamic models to generate risk maps for PRRS outbreaks and reconstructed the evolutionary history of three selected phylogenetic clades (A, B and C). High-risk areas for PRRS were best-predicted by pig density and climate seasonality and included Minnesota, Iowa and South Dakota. Phylodynamic models demonstrated that the geographical spread of the three clades followed a heterogeneous spatial diffusion process. Furthermore, PRRS viruses were characterized by typical seasonality in their population size. However, endemic strains were characterized by a substantially slower population growth and evolutionary rates, as well as smaller spatial dispersal rates when compared to emerging strains. We demonstrated the prospects of combining inferences derived from two unique analytical methods to inform decisions related to risk-based interventions of an important pathogen affecting one of the largest food animal industries in the world.