Utilizing machine learning and hemagglutinin sequences to identify likely hosts of influenza H3Nx viruses.

Influenza is a disease that represents both a public health and agricultural risk with pandemic potential. Among the subtypes of influenza A virus, H3 influenza virus can infect many avian and mammalian species and is therefore a virus of interest to human and veterinary public health. The primary goal of this study was to train and validate classifiers for the identification of the most likely host species using the hemagglutinin gene segment of H3 viruses. A five-step process was implemented, which included training four machine learning classifiers, testing the classifiers on the validation dataset, and further exploration of the best-performing model on three additional datasets. The gradient boosting machine classifier showed the highest host-classification accuracy with a 98.0 % (95 % CI [97.01, 98.73]) correct classification rate on an independent validation dataset. The classifications were further analyzed using the predicted probability score which highlighted sequences of particular interest. These sequences were both correctly and incorrectly classified sequences that showed considerable predicted probability for multiple hosts. This showed the potential of using these classifiers for rapid sequence classification and highlighting sequences of interest. Additionally, the classifiers were tested on a separate swine dataset composed of H3N2 sequences from 1998 to 2003 from the United States of America, and a separate canine dataset composed of canine H3N2 sequences of avian origin. These two datasets were utilized to look at the applications of predicted probability and host convergence over time. Lastly, the classifiers were used on an independent dataset of environmental sequences to explore the host identification of environmental sequences. The results of these classifiers show the potential for machine learning to be used as a host identification technique for viruses of unknown origin on a species-specific level.

Prevalence of Adult Honey Bee (Apis mellifera L.) Pests and Pathogens in the Five Beekeeping Regions of Mexico.

Mexico is a major honey producer, but not much information exists about the health status of honey bees (Apis mellifera L.) in the country. This study was conducted to determine the sanitary status of adult honey bees in Mexico's five beekeeping regions. Samples from 369 apiaries were diagnosed to identify pathogens such as Varroa destructor, which was quantified, Acarapis woodi, Nosema spp., and five viruses. Colonies were also inspected for the presence of the small hive beetle (SHB), Aethina tumida. Varroa destructor was found in 83.5% of the apiaries, with the Pacific Coast region having the highest prevalence (>95%) and rates (4.5% ± 0.6). Acarapis woodi was detected in only one apiary from the Pacific Coast, whereas Nosema spp. were prevalent in 48.5% of the apiaries, with the highest and lowest frequencies in the Yucatan Peninsula and North regions (64.6% and 10.2%, respectively). For viruses, deformed wing virus (DWV) was detected in 26.1% of the apiaries, with the highest frequency in the Pacific Coast region (44.7%). Israeli acute paralysis virus (IAPV) was diagnosed in 3.2% of the samples and sacbrood bee virus (SBV) in 23.3% of them, with the highest frequency in the High Plateau region (36.4%). Chronic bee paralysis and Kashmir bee viruses were not detected. SHB prevalence was 25.2% nationwide, with the highest frequency in the Yucatan Peninsula (39.2%). This study shows that the most common parasites of adult honey bees in Mexico are V. destructor and Nosema spp., and that the most prevalent virus is DWV, whereas SHB is highly prevalent in the Yucatan Peninsula. This information could be useful to design disease control strategies for honey bee colonies in different regions of Mexico.

Development of interactive dashboards for monitoring endemic animal pathogens in Ontario, Canada: Ontario interactive animal pathogen dashboards.

The advancement of web-based technologies makes it possible to build user interfaces or web pages that present and summarize complex data in easy-to-read graphical formats that emphasize key information. Taking advantage of this technologic progress, we addressed the need for real-time visualizations of trends for major pathogens in the largest livestock industries in Ontario: poultry, swine, and cattle. These visualizations were built using test data from the laboratory information management system of the Animal Health Laboratory at the University of Guelph, a large veterinary diagnostic laboratory in Ontario. The data were processed using R software and used to construct interactive and dynamic visualizations using Tableau Desktop v.2021.4 (Tableau Software). We designed 12 dashboards: in chickens-influenza A virus, fowl adenovirus, infectious bronchitis virus, and infectious laryngotracheitis virus; in turkeys-influenza A virus; in swine, influenza A virus, rotavirus, and porcine reproductive and respiratory syndrome virus; in cattle-bovine viral diarrhea virus, Mycoplasma bovis, Salmonella Dublin in individual samples, and Salmonella Dublin in bulk tank milk samples. Data for each pathogen are presented in 2 dashboards. One shows the data of the last 10 y (general view) and the other the data of the last 3 y, but in more detail (comprehensive view). Information on gaining access to all dashboards is available at https://iapd.lsd.uoguelph.ca/. The visualizations provide near-real-time access to aggregated assay results for selected pathogens for veterinarians, animal health regulatory agencies, researchers, and other users who are interested in livestock pathogen surveillance.

The Fungus Nosema ceranae and a Sublethal Dose of the Neonicotinoid Insecticide Thiamethoxam Differentially Affected the Health and Immunity of Africanized Honey Bees.

Honey bees (Apis mellifera L.) are affected by different biotic and abiotic stressors, such as the fungus Nosema ceranae and neonicotinoid insecticides, that negatively impact their health. However, most studies so far conducted have focused on the effect of these stressors separately and in European honey bees. Therefore, this study was conducted to analyze the impact of both stressors, singly and in combination, on honey bees of African descent that have demonstrated resistance to parasites and pesticides. Africanized honey bees (AHBs, Apis mellifera scutellata Lepeletier) were inoculated with N. ceranae (1 × 105 spores/bee) and/or chronically exposed for 18 days to a sublethal dose of thiamethoxam (0.025 ng/bee) to evaluate their single and combined effects on food consumption, survivorship, N. ceranae infection, and immunity at the cellular and humoral levels. No significant effects by any of the stressors were found for food consumption. However, thiamethoxam was the main stressor associated to a significant decrease in AHB survivorship, whereas N. ceranae was the main stressor affecting their humoral immune response by upregulating the expression of the gene AmHym-1. Additionally, both stressors, separately and combined, significantly decreased the concentration of haemocytes in the haemolymph of the bees. These findings indicate that N. ceranae and thiamethoxam differentially affect the lifespan and immunity of AHBs and do not seem to have synergistic effects when AHBs are simultaneously exposed to both stressors.

Genotype, but Not Climate, Affects the Resistance of Honey Bees (Apis mellifera) to Viral Infections and to the Mite Varroa destructor.

This study was conducted to analyze the effect of genotype and climate on the resistance of honey bee (Apis mellifera) colonies to parasitic and viral diseases. The prevalence and intensity of parasitism by Varroa destructor, or infection by Nosema spp., and four honey bee viruses were determined in 365 colonies of predominantly European or African ancestry (descendants of A. m. scutellata) in subtropical and temperate regions of Mexico. Varroa destructor was the most prevalent parasite (95%), whilst N. ceranae was the least prevalent parasite (15%). Deformed wing virus (DWV) and black queen cell virus (BQCV) were the only viruses detected, at frequencies of 38% and 66%, respectively. Varroa destructor was significantly more prevalent in colonies of European ancestry (p < 0.05), and the intensity of parasitism by V. destructor or infection by DWV and BQCV was also significantly higher in colonies of European descent than in African descent colonies (p < 0.01), although no genotype−parasite associations were found for N. ceranae. Additionally, significant and positive correlations were found between V. destructor and DWV levels, and the abundance of these pathogens was negatively correlated with the African ancestry of colonies (p < 0.01). However, there were no significant effects of environment on parasitism or infection intensity for the colonies of both genotypes. Therefore, it is concluded that the genotype of honey bee colonies, but not climate, influences their resistance to DWV, BQCV, and V. destructor.

Detection and Concentration of Neonicotinoids and Other Pesticides in Honey from Honey Bee Colonies Located in Regions That Differ in Agricultural Practices: Implications for Human and Bee Health.

This is a preliminary study conducted to analyze the presence and concentration of pesticides in honey obtained from honey bee colonies located in two regions with managed ecosystems that differ in the intensity and technification of agricultural practices. Fourteen pesticides at variable concentrations were detected in 63% of the samples analyzed. The pesticides most frequently found at higher concentrations were insecticides (neonicotinoids, followed by organophosphates), herbicides, and fungicides. The number, frequency, and concentration of pesticides were higher in samples collected from hives located where intensive and highly-technified agriculture is practiced. Forty-three percent of the samples from that zone had residues of imidacloprid, compared with only 13% of the samples from the less-technified zone. Furthermore, 87.5% of those samples had imidacloprid concentrations that were above sublethal doses for honey bees (>0.25 ng/g) but that are not considered hazardous to human health by the European Commission. The results of this study suggest that honey can be used as a bioindicator of environmental contamination by pesticides, which highlights the need to continue monitoring contaminants in this product to determine the risks of pesticide impacts on pollinator health, on ecosystems, and on their potential implications to human health and other non-target organisms.

The impact of the initial public health response to COVID-19 on swine health surveillance in Ontario.

COVID-19 restrictions and the pandemic have affected animal health and food production through the disease's effects on human activities. COVID-19 impact on swine health surveillance can be assessed by investigating submissions and test positivity for pathogens before and after COVID-19 restrictions. PRRSV, Influenza A virus, Mycoplasma hyopneumoniae and PCV-2 are considered important and economically challenging respiratory diseases for the swine populations. By reviewing test results from swine samples submitted for diagnostic testing to a regional diagnostic laboratory, and by assessing total submissions, total positive tests, and the proportion of positive tests at weekly intervals with time series techniques and generalized linear regression models, we evaluated COVID-19's impact on the monitoring of these respiratory pathogens in Ontario, Canada. We classified weeks that fell from week 12 through week 24 in each year as pandemic equivalent weeks and the non-pandemic weeks included all other weeks. The pandemic period in 2020 resulted in a significantly higher number of submissions (p < 0.05) and PRRSV positive submission counts (p < 0.05) when compared to equivalent time periods in previous years; however, no changes could be detected in the odds of weekly PRRSV submission positivity. Weekly positive proportions of PCV-2 tests were higher during the pandemic period in 2020 compared with the pandemic equivalent period in 2018 and 2017. The counts of submissions that requested tests for PRRSV, Influenza A virus and M. hyopneumonia combined, as well as the number of submissions and the proportions of submissions that tested negative for these multiple respiratory pathogens were not significantly different between the pandemic period in 2020 and other periods examined. Our findings indicate that swine producers, in conjunction with various private and public veterinary support services, continued monitoring and performing diagnostic screening on farms for economically important animal diseases despite complications resulting from COVID-19 public health restrictions. PRRSV continues to have a serious impact on swine health. The absence of an increased proportion of negative tests for individual or groups of pathogens, or an accompanying increase in submissions during the 2020 pandemic period suggests that no new undetected pathogens with an impact on respiratory signs in swine were introduced during this time.

Effect of feeding chitosan or peptidoglycan on Nosema ceranae infection and gene expression related to stress and the innate immune response of honey bees (Apis mellifera).

Nosema ceranae is a microsporidian parasite that causes nosema disease, an infection of the honey bee (Apis mellifera) midgut. Two pathogen-associated molecular patterns (PAMPs), chitosan and peptidoglycan, and N. ceranae spores were fed to worker bees in sucrose syrup and compared to non-inoculated and N. ceranae-inoculated bees without PAMPs. Both chitosan and peptidoglycan significantly increased bee survivorship and reduced spore numbers due to N. ceranae infection. To determine if these results were related to changes in health status, expression of the immune-related genes, hymenoptaecin and defensin2, and the stress tolerance-related gene, blue cheese, was compared to that of control bees. Compared to the inoculated control, bees with the dose of chitosan that significantly reduced N. ceranae spore numbers showed lower expression of hymenoptaecin and defensin2 early after infection, higher expression mid-infection of defensin2 and lower expression of all three genes late in infection. In contrast, higher expression of defensin2 early in the infection and all three genes late in the infection was observed with peptidoglycan treatment. Changes late in the parasite multiplication stage when mature spores would be released from ruptured host cells are less likely to have contributed to reduced spore production. Based on these results, it is concluded that feeding bees chitosan or peptidoglycan can reduce N. ceranae infection, which is at least partially related to altering the health of the bee by inducing immune and stress-related gene expression.

Nosema ceranae Infections in Honey Bees (Apis mellifera) Treated with Pre/Probiotics and Impacts on Colonies in the Field.

Alternatives to the antibiotic fumagillin for the control of Nosema ceranae, a gut parasite of the honey bee, are needed. The prebiotics eugenol, chitosan, and naringenin and the probiotic Protexin® (Enterococcus faecium) provided in sugar syrup or protein patty either in spring or fall were evaluated for their effects on N. ceranae infection, colony population, honey yield and winter survivorship using field colonies. In the first year, spring treatments with eugenol, naringenin, and Protexin® significantly reduced N. ceranae infection and increased honey production, while Protexin® also increased adult bee populations and chitosan was ineffective. Fall treatments increased survivorship and decreased N. ceranae infection the following spring. In the second year, selected compounds were further tested with a larger number of colonies per treatment and only protein patty used in the spring and sugar syrup in the fall. Protexin® and naringenin significantly decreased N. ceranae infections and increased the population of adult bees after spring treatment, but did not affect honey yields. There were no differences between treatments for colony winter mortality, but surviving colonies that had been treated with Protexin® and naringenin were significantly more populated and had lower N. ceranae spore counts than control, non-treated colonies. Protexin® and naringenin were the most promising candidates for controlling N. ceranae and promoting honey bee populations, warranting further investigation. Future research should investigate the optimal colony dose and treatment frequency to maximize colony health.

Nosema ceranae causes cellular immunosuppression and interacts with thiamethoxam to increase mortality in the stingless bee Melipona colimana.

The microsporidian parasite Nosema ceranae and neonicotinoid insecticides affect the health of honey bees (Apis mellifera). However, there is limited information about the effect of these stressors on other pollinators such as stingless bees (Hymenoptera: Meliponini). We examined the separate and combined effects of N. ceranae and the neonicotinoid thiamethoxam at field-exposure levels on the survivorship and cellular immunity (hemocyte concentration) of the stingless bee Melipona colimana. Newly-emerged bees were subjected to four treatments provided in sucrose syrup: N. ceranae spores, thiamethoxam, thiamethoxam and N. ceranae, and control (bees receiving only syrup). N. ceranae developed infections of > 467,000 spores/bee in the group treated with spores only. However, in the bees subjected to both stressors, infections were < 143,000 spores/bee, likely due to an inhibitory effect of thiamethoxam on the microsporidium. N. ceranae infections did not affect bee survivorship, but thiamethoxam plus N. ceranae significantly increased mortality. Hemocyte counts were significantly lower in N. ceranae infected-bees than in the other treatments. These results suggest that N. ceranae may infect, proliferate and cause cellular immunosuppression in stingless bees, that exposure to sublethal thiamethoxam concentrations is toxic to M. colimana when infected with N. ceranae, and that thiamethoxam restrains N. ceranae proliferation. These findings have implications on pollinators' conservation.

Seasonality of Nosema ceranae Infections and Their Relationship with Honey Bee Populations, Food Stores, and Survivorship in a North American Region.

Nosema ceranae is an emerging pathogen of the western honey bee (Apis mellifera L.), and thus its seasonality and impact on bee colonies is not sufficiently documented for North America. This study was conducted to determine the infection intensity, prevalence, and viability of N. ceranae in >200 honey bee colonies during spring, summer, and fall, in a North American region. We also determined the relationship of N. ceranae infections with colony populations, food stores, bee survivorship, and overwinter colony mortality. The highest rates of N. ceranae infection, prevalence, and spore viability were found in the spring and summer, while the lowest were recorded in the fall. N. ceranae spore viability was significantly correlated with its prevalence and infection intensity in bees. Threshold to high levels of N. ceranae infections (>1,000,000 spores/bee) were significantly associated with reduced bee populations and food stores in colonies. Furthermore, worker bee survivorship was significantly reduced by N. ceranae infections, although no association between N. ceranae and winter colony mortality was found. It is concluded that N. ceranae infections are highest in spring and summer and may be detrimental to honey bee populations and colony productivity. Our results support the notion that treatment is justified when infections of N. ceranae exceed 1,000,000 spores/bee.

Impact of Varroa destructor and deformed wing virus on emergence, cellular immunity, wing integrity and survivorship of Africanized honey bees in Mexico.

The ectoparasitic mite Varroa destructor is the primary health problem of honey bees (Apis mellifera) worldwide. Africanized honey bees in Brazil have demonstrated tolerance to the mite, but there is controversy about the degree of mite tolerance of Africanized bees in other countries. This study was conducted to quantify the effect of V. destructor parasitism on emergence, hemocyte concentration, wing integrity and longevity of Africanized honey bees in Mexico. Africanized bee brood were artificially infested with V. destructor mites and held in an incubator until emergence as adults and compared to non-infested controls. Deformed wing virus (DWV) presence was determined in the mites used to infest the bees. After emergence, the bees were maintained in an incubator to determine survivorship. The percentage of worker bees that emerged from parasitized cells (69%) was significantly lower than that of bees emerged from non-infested cells (96%). Newly-emerged parasitized bees had a significantly lower concentration of hemocytes in the hemolymph than non-parasitized bees. Additionally, the proportion of bees with deformed wings that emerged from V. destructor-parasitized cells was significantly higher (54%) than that of the control group (0%). The mean survival time of bees that emerged from infested and non-infested cells was 8.5 ±â€¯0.3 and 14.4 ±â€¯0.4 days, respectively, and the difference was significant. We conclude that V. destructor parasitism and DWV infections kill, cause deformities and inhibit cellular immunity in developing Africanized honey bees, and significantly reduce the lifespan of adult bees in Mexico. These results suggest that the tolerance of Africanized bees to V. destructor is related to adult bee mechanisms.

Assessment of autoregressive integrated moving average (ARIMA), generalized linear autoregressive moving average (GLARMA), and random forest (RF) time series regression models for predicting influenza A virus frequency in swine in Ontario, Canada.

Influenza A virus commonly circulating in swine (IAV-S) is characterized by large genetic and antigenic diversity and, thus, improvements in different aspects of IAV-S surveillance are needed to achieve desirable goals of surveillance such as to establish the capacity to forecast with the greatest accuracy the number of influenza cases likely to arise. Advancements in modeling approaches provide the opportunity to use different models for surveillance. However, in order to make improvements in surveillance, it is necessary to assess the predictive ability of such models. This study compares the sensitivity and predictive accuracy of the autoregressive integrated moving average (ARIMA) model, the generalized linear autoregressive moving average (GLARMA) model, and the random forest (RF) model with respect to the frequency of influenza A virus (IAV) in Ontario swine. Diagnostic data on IAV submissions in Ontario swine between 2007 and 2015 were obtained from the Animal Health Laboratory (University of Guelph, Guelph, ON, Canada). Each modeling approach was examined for predictive accuracy, evaluated by the root mean square error, the normalized root mean square error, and the model's ability to anticipate increases and decreases in disease frequency. Likewise, we verified the magnitude of improvement offered by the ARIMA, GLARMA and RF models over a seasonal-naïve method. Using the diagnostic submissions, the occurrence of seasonality and the long-term trend in IAV infections were also investigated. The RF model had the smallest root mean square error in the prospective analysis and tended to predict increases in the number of diagnostic submissions and positive virological submissions at weekly and monthly intervals with a higher degree of sensitivity than the ARIMA and GLARMA models. The number of weekly positive virological submissions is significantly higher in the fall calendar season compared to the summer calendar season. Positive counts at weekly and monthly intervals demonstrated a significant increasing trend. Overall, this study shows that the RF model offers enhanced prediction ability over the ARIMA and GLARMA time series models for predicting the frequency of IAV infections in diagnostic submissions.

Environmental and social determinants of population vulnerability to Zika virus emergence at the local scale.

BACKGROUND: Zika virus (ZIKV) spread rapidly in the Americas in 2015. Targeting effective public health interventions for inhabitants of, and travellers to and from, affected countries depends on understanding the risk of ZIKV emergence (and re-emergence) at the local scale. We explore the extent to which environmental, social and neighbourhood disease intensity variables influenced emergence dynamics. Our objective was to characterise population vulnerability given the potential for sustained autochthonous ZIKV transmission and the timing of emergence. Logistic regression models estimated the probability of reporting at least one case of ZIKV in a given municipality over the course of the study period as an indicator for sustained transmission; while accelerated failure time (AFT) survival models estimated the time to a first reported case of ZIKV in week t for a given municipality as an indicator for timing of emergence. RESULTS: Sustained autochthonous ZIKV transmission was best described at the temporal scale of the study period (almost one year), such that high levels of study period precipitation and low mean study period temperature reduced the probability. Timing of ZIKV emergence was best described at the weekly scale for precipitation in that high precipitation in the current week delayed reporting. Both modelling approaches detected an effect of high poverty on reducing/slowing case detection, especially when inter-municipal road connectivity was low. We also found that proximity to municipalities reporting ZIKV had an effect to reduce timing of emergence when located, on average, less than 100 km away. CONCLUSIONS: The different modelling approaches help distinguish between large temporal scale factors driving vector habitat suitability and short temporal scale factors affecting the speed of spread. We find evidence for inter-municipal movements of infected people as a local-scale driver of spatial spread. The negative association with poverty suggests reduced case reporting in poorer areas. Overall, relatively simplistic models may be able to predict the vulnerability of populations to autochthonous ZIKV transmission at the local scale.

Differential responses of Africanized and European honey bees (Apis mellifera) to viral replication following mechanical transmission or Varroa destructor parasitism.

For the first time, adults and brood of Africanized and European honey bees (Apis mellifera) were compared for relative virus levels over 48 h following Varroa destructor parasitism or injection of V. destructor homogenate. Rates of increase of deformed wing virus (DWV) for Africanized versus European bees were temporarily lowered for 12h with parasitism and sustainably lowered over the entire experiment (48 h) with homogenate injection in adults. The rates were also temporarily lowered for 24h with parasitism but were not affected by homogenate injection in brood. Rates of increase of black queen cell virus (BQCV) for Africanized versus European bees were similar with parasitism but sustainably lowered over the entire experiment with homogenate injection in adults and were similar for parasitism and homogenate injection in brood. Analyses of sac brood bee virus and Israeli acute paralysis virus were limited as detection did not occur after both homogenate injection and parasitism treatment, or levels were not significantly higher than those following control buffer injection. Lower rates of replication of DWV and BQCV in Africanized bees shows that they may have greater viral resistance, at least early after treatment.

Genotypic variability and relationships between mite infestation levels, mite damage, grooming intensity, and removal of Varroa destructor mites in selected strains of worker honey bees (Apis mellifera L.).

The objective of this study was to demonstrate genotypic variability and analyze the relationships between the infestation levels of the parasitic mite Varroa destructor in honey bee (Apis mellifera) colonies, the rate of damage of fallen mites, and the intensity with which bees of different genotypes groom themselves to remove mites from their bodies. Sets of paired genotypes that are presumably susceptible and resistant to the varroa mite were compared at the colony level for number of mites falling on sticky papers and for proportion of damaged mites. They were also compared at the individual level for intensity of grooming and mite removal success. Bees from the "resistant" colonies had lower mite population rates (up to 15 fold) and higher percentages of damaged mites (up to 9 fold) than bees from the "susceptible" genotypes. At the individual level, bees from the "resistant" genotypes performed significantly more instances of intense grooming (up to 4 fold), and a significantly higher number of mites were dislodged from the bees' bodies by intense grooming than by light grooming (up to 7 fold) in all genotypes. The odds of mite removal were high and significant for all "resistant" genotypes when compared with the "susceptible" genotypes. The results of this study strongly suggest that grooming behavior and the intensity with which bees perform it, is an important component in the resistance of some honey bee genotypes to the growth of varroa mite populations. The implications of these results are discussed.