Distinctive egg-laying patterns in terminal versus non-terminal periods in three fruit fly species.

The specific objective of this study was to use a logistic regression model for determining the degree to which egg laying patterns of individual females at the end of life (i.e., terminal segments) in each of three different fruit fly species could be distinguished from the egg-laying patterns over a similar period in midlife (i.e., non-terminal segments). Extracting data from large-scale databases for 11-day terminal and 11-day non-terminal segments in the vinegar fly (Drosophila melanogaster), the Mexican fruit fly (Anastrepha ludens) and the Mediterranean fruit fly (Ceratitis capitata) and organizing the model's results in a 2 × 2 contingency table, we found that: (1) daily egg-laying patterns in fruit flies can be used to distinguish terminal from non-terminal periods; (2) the overall performance metrics such as precision, accuracy, false positives and true negatives depended heavily on species; (3) differentiating between terminal and non-terminal segments is more difficult when flies die at younger ages; and (4) among the three species the best performing metrics including accuracy and precision were those produced using data on D. melanogaster. We conclude that, although the reliability of the prediction of whether a segment occurred at the end of life is relatively high for most species, it does not follow precisely predicting remaining life will also be highly reliable since classifying an end of life period is a fundamentally different challenge than is predicting an exact day of death.

The failure of success: cyclic recurrences of a globally invasive pest.

In the six decades since 1960, the oriental fruit fly, Bactrocera dorsalis (Hendel), has been announced successfully eradicated in California by the U.S. Department of Agriculture a total of 564 times. This includes eradication declarations in one city a total of 25 different years, in 12 cities 8-19 different years, and in 101 cities 2-7 different years. We here show that the false negatives in declaring elimination success hinge on the easily achieved regulatory criteria, which have virtually guaranteed the failure of complete extirpation of this pest. Analyses of the time series of fly detection over California placed on a grid of 100-km2 cells revealed (1) partial success of the eradication program in controlling the invasion of the oriental fruit fly; (2) low prevalence of the initial detection in these cells is often followed by high prevalence of recurrences; (3) progressively shorter intervals between years of consecutive detections; and (4) high likelihood of early-infested cells also experiencing the most frequent outbreaks. Facing the risk of recurrent invasions, such short-term eradication programs have only succeeded annually according to the current regulatory criteria but have failed to achieve the larger goal of complete extirpation of the oriental fruit fly. Based on the components and running costs of the current programs, we further estimated the efficiency of eradication programs with different combinations of eradication radius, duration, and edge impermeability in reducing invasion recurrences and slowing the spread of the oriental fruit fly. We end with policy implications including the need for agricultural agencies worldwide to revisit eradication protocols in which monitoring and treatments are terminated when the regulatory criteria for declaring eradication are met. Our results also have direct implications to invasion biologists and agriculture policy makers regarding long-term risks of short-term expediency.

An economic analysis of a contingency model utilising vaccination for the control of equine influenza in a non-endemic country.

BACKGROUND: Equine influenza (EI) is an infectious respiratory disease of horses that has never been reported in New Zealand (NZ). However, the 2007 EI outbreak in Australia, previously EI free, spurred the NZ government and stakeholders into evaluating alternative EI control strategies in order to economically justify any future decision to eradicate or manage EI. To build on the policy debate, this paper presents an epinomic (epidemiologic and economic) modelling approach to evaluate alternative control strategies. An epidemiologic model to determine how alternative EI control strategies influence the distribution of EI. Model results were then input into a cost-benefit analysis framework, to identify the return and feasibility of alternative EI eradication strategies in NZ. METHODS: The article explores nine alternative eradication scenarios and two baseline strategies. The alternative scenarios consisted of three vaccination strategies (suppressive, protective or targeted) starting at three time points to reflect the commercial breeding-cycle. These alternatives were compared to two breeding-cycle adjusted baselines: movement restriction in the breeding season (August to January) or non-breeding season (February to July). The economic loss parameters were incursion response, impact to the commercial racing industry (breeding, sales and racing), horse morbidity and mortality, and compensation to industry participants. RESULTS AND CONCLUSIONS: Results suggest that the economic viability of the EI eradication programme is dependent on when within the breeding-cycle the EI outbreak occurs. If an outbreak were to occur, the return on each dollar invested for protective or suppressive vaccination strategies would be between NZD$3.67 to NZD$4.89 and between NZD$3.08 to NZD$3.50 in the breeding and non-breeding seasons, respectively. Therefore, protective or suppressive vaccination strategies could be prioritised, regardless of season. As multiple industry stakeholders benefit from these strategies, the study will enable policy development and to better formulate a user-pays eradication programme.

Spatial clustering of pathology submissions during the initial introduction and spread of avian influenza H5N1 in poultry in Nigeria in 2006-2007.

Highly pathogenic avian influenza (HPAI) virus H5N1 spread throughout Nigeria between 2006 and 2007. Bird samples collected across the country were submitted through the free-of-charge (FOC) program to the National Veterinary Research Institute, Vom (NVRI-Vom) laboratory. The present article describes the spatial distributions and evaluated clustering of the FOC submissions from poultry farms at the global, local, and focal levels between 2006 and 2007 epidemic in Nigeria. Spatial statistics evaluating clustering of the FOC submissions were implemented using the Moran's I test, the purely spatial cluster analysis with the SaTScan Poisson model, and the Bithell's linear score test. A significant global clustering of the FOC submissions was observed. Significant local clusters of submissions were observed in the North-East, North-Central, and South-West zones. There was significant decline in FOC submissions with increasing distance from NVRI-Vom. These results indicated that the geographic area of influence of the FOC submission program in Nigeria was limited to regions closer to the diagnostic laboratory. This work provides a detailed insight into the surveillance activities during the HPAI outbreaks in Nigeria, and should assist policy-makers and field veterinarians to improve the effectiveness of national eradication plans in the face of any outbreak of animal diseases.

Financial Impact of Foot-and-mouth disease outbreaks on pig farms in the Republic of Korea, 2014/2015.

The financial impact of foot-and-mouth disease (FMD) that occurred in 180 piggeries (100 farrow-to-finish and 80 fattening farms) confirmed infected during the 2014/2015 epidemic in the Republic of Korea was estimated at the farm level. The median loss due to slaughtering of pigs prior to their expected market weights was US$ 71.8 (uncovered compensation-compensation loss) plus US$ 57.3 (foregone net gain) per pig. Median loss per farm was US$ 27,487 (55.6% of total loss) for compensation and US$ 15,925 (44.4%) for foregone net gain. The total loss per farm (median, 25th-75th percentile) was US$ 43,822 (9,767-115,893), which represented 49.4% (11.5-112.8) of the annual net gain of pig farms. The total financial loss in 180 FMD outbreak pig farms was US$ 25.2 million, which was nearly one-half of the control cost (US$ 58.3 million) spent by the Korean government on this epidemic. The findings in this study should help planning to help reduce the impact at the farm level in the Republic of Korea in the future.

Evaluating the efficacy of regionalisation in limiting high-risk livestock trade movements.

Many countries implement regionalisation as a measure to control economically important livestock diseases. Given that regionalisation highlights the difference in disease risk between animal subpopulations, this may discourage herd managers in low-risk areas from purchasing animals from high-risk areas to protect the disease-free status of their herds. Using bovine tuberculosis (bTB) in New Zealand as a case example, we develop a novel network simulation model to predict how much the frequency of cattle movements between different disease control areas (DCAs) could theoretically change if herd managers adopted the safest practices (preferentially purchasing cattle from areas with the lowest risk of bTB), if herd managers adopted the riskiest practices (preferentially purchasing cattle from areas with the greatest risk of bTB), or if herd managers made trade decisions completely at random (purchasing cattle without consideration for bTB disease risk). A modified configuration wiring algorithm was used in the network simulation model to preserve key temporal, spatial, and demographic attributes of cattle movement patterns. The simulated frequencies of cattle movements between DCAs in each of the three behavioural scenarios were compared with the actual frequency of cattle movements that occurred between 1st July 2010 and 30th June 2011. Our results showed that the observed frequency of cattle movements from high-risk areas into low-risk areas was significantly less than if trade decisions were made completely at random, but still significantly greater than if herd managers made the safest possible trade decisions. This suggests that while New Zealand cattle farmers may have adopted risk-averse trading behaviour in response to regionalisation, there are other underlying factors driving livestock trade, such as established supplier-buyer relationships and heterogeneous individual perceptions towards disease risk, which may reduce the potential efficacy of regionalisation as a disease control strategy. Physical constraints and socio-psychological factors that determine herd managers' livestock trading behaviour warrant further studies to better understand how herd managers respond to future livestock disease regulations. The flexibility of a network re-wiring framework presented in this study allows such a behavioural response to be incorporated into a disease simulation model, which will in turn facilitate a better evaluation of disease control strategies.

Coastal development and precipitation drive pathogen flow from land to sea: evidence from a Toxoplasma gondii and felid host system.

Rapidly developing coastal regions face consequences of land use and climate change including flooding and increased sediment, nutrient, and chemical runoff, but these forces may also enhance pathogen runoff, which threatens human, animal, and ecosystem health. Using the zoonotic parasite Toxoplasma gondii in California, USA as a model for coastal pathogen pollution, we examine the spatial distribution of parasite runoff and the impacts of precipitation and development on projected pathogen delivery to the ocean. Oocysts, the extremely hardy free-living environmental stage of T. gondii shed in faeces of domestic and wild felids, are carried to the ocean by freshwater runoff. Linking spatial pathogen loading and transport models, we show that watersheds with the highest levels of oocyst runoff align closely with regions of increased sentinel marine mammal T. gondii infection. These watersheds are characterized by higher levels of coastal development and larger domestic cat populations. Increases in coastal development and precipitation independently raised oocyst delivery to the ocean (average increases of 44% and 79%, respectively), but dramatically increased parasite runoff when combined (175% average increase). Anthropogenic changes in landscapes and climate can accelerate runoff of diverse pathogens from terrestrial to aquatic environments, influencing transmission to people, domestic animals, and wildlife.

Decision-making for foot-and-mouth disease control: Objectives matter.

Formal decision-analytic methods can be used to frame disease control problems, the first step of which is to define a clear and specific objective. We demonstrate the imperative of framing clearly-defined management objectives in finding optimal control actions for control of disease outbreaks. We illustrate an analysis that can be applied rapidly at the start of an outbreak when there are multiple stakeholders involved with potentially multiple objectives, and when there are also multiple disease models upon which to compare control actions. The output of our analysis frames subsequent discourse between policy-makers, modellers and other stakeholders, by highlighting areas of discord among different management objectives and also among different models used in the analysis. We illustrate this approach in the context of a hypothetical foot-and-mouth disease (FMD) outbreak in Cumbria, UK using outputs from five rigorously-studied simulation models of FMD spread. We present both relative rankings and relative performance of controls within each model and across a range of objectives. Results illustrate how control actions change across both the base metric used to measure management success and across the statistic used to rank control actions according to said metric. This work represents a first step towards reconciling the extensive modelling work on disease control problems with frameworks for structured decision making.

Using molecular epidemiology to track Toxoplasma gondii from terrestrial carnivores to marine hosts: implications for public health and conservation.

BACKGROUND: Environmental transmission of the zoonotic parasite Toxoplasma gondii, which is shed only by felids, poses risks to human and animal health in temperate and tropical ecosystems. Atypical T. gondii genotypes have been linked to severe disease in people and the threatened population of California sea otters. To investigate land-to-sea parasite transmission, we screened 373 carnivores (feral domestic cats, mountain lions, bobcats, foxes, and coyotes) for T. gondii infection and examined the distribution of genotypes in 85 infected animals sampled near the sea otter range. METHODOLOGY/PRINCIPAL FINDINGS: Nested PCR-RFLP analyses and direct DNA sequencing at six independent polymorphic genetic loci (B1, SAG1, SAG3, GRA6, L358, and Apico) were used to characterize T. gondii strains in infected animals. Strains consistent with Type X, a novel genotype previously identified in over 70% of infected sea otters and four terrestrial wild carnivores along the California coast, were detected in all sampled species, including domestic cats. However, odds of Type X infection were 14 times higher (95% CI: 1.3-148.6) for wild felids than feral domestic cats. Type X infection was also linked to undeveloped lands (OR = 22, 95% CI: 2.3-250.7). A spatial cluster of terrestrial Type II infection (P = 0.04) was identified in developed lands bordering an area of increased risk for sea otter Type II infection. Two spatial clusters of animals infected with strains consistent with Type X (P ≤ 0.01) were detected in less developed landscapes. CONCLUSIONS: Differences in T. gondii genotype prevalence among domestic and wild felids, as well as the spatial distribution of genotypes, suggest co-existing domestic and wild T. gondii transmission cycles that likely overlap at the interface of developed and undeveloped lands. Anthropogenic development driving contact between these cycles may increase atypical T. gondii genotypes in domestic cats and facilitate transmission of potentially more pathogenic genotypes to humans, domestic animals, and wildlife.

A spatial risk assessment of bighorn sheep extirpation by grazing domestic sheep on public lands.

Bighorn sheep currently occupy just 30% of their historic distribution, and persist in populations less than 5% as abundant overall as their early 19th century counterparts. Present-day recovery of bighorn sheep populations is in large part limited by periodic outbreaks of respiratory disease, which can be transmitted to bighorn sheep via contact with domestic sheep grazing in their vicinity. In order to assess the viability of bighorn sheep populations on the Payette National Forest (PNF) under several alternative proposals for domestic sheep grazing, we developed a series of interlinked models. Using telemetry and habitat data, we characterized herd home ranges and foray movements of bighorn sheep from their home ranges. Combining foray model movement estimates with known domestic sheep grazing areas (allotments), a Risk of Contact Model estimated bighorn sheep contact rates with domestic sheep allotments. Finally, we used demographic and epidemiologic data to construct population and disease transmission models (Disease Model), which we used to estimate bighorn sheep persistence under each alternative grazing scenario. Depending on the probability of disease transmission following interspecies contact, extirpation probabilities for the seven bighorn sheep herds examined here ranged from 20% to 100%. The Disease Model allowed us to assess the probabilities that varied domestic sheep management scenarios would support persistent populations of free-ranging bighorn sheep.

Evaluation of the benefit of emergency vaccination in a foot-and-mouth disease free country with low livestock density.

Foot-and-mouth disease (FMD) is highly contagious and one of the most economically devastating diseases of cloven-hoofed animals. Scientific-based preparedness about how to best control the disease in a previously FMD-free country is therefore essential for veterinary services. The present study used a spatial, stochastic epidemic simulation model to compare the effectiveness of emergency vaccination with conventional (non-vaccination) control measures in Switzerland, a low-livestock density country. Model results revealed that emergency vaccination with a radius of 3 km or 10 km around infected premises (IP) did not significantly reduce either the cumulative herd incidence or epidemic duration if started in a small epidemic situation where the number of IPs is still low. However, in a situation where the epidemic has become extensive, both the cumulative herd incidence and epidemic duration are reduced significantly if vaccination were implemented with a radius of 10 km around IPs. The effect of different levels of conventional strategy measures was also explored for the non-vaccination strategy. It was found that a lower compliance level of farmers for movement restrictions and delayed culling of IPs significantly increased both the cumulative IP incidence and epidemic duration. Contingency management should therefore focus mainly on improving conventional strategies, by increasing disease awareness and communication with stakeholders and preparedness of culling teams in countries with a livestock structure similar to Switzerland; however, emergency vaccination should be considered if there are reasons to believe that the epidemic may become extensive, such as when disease detection has been delayed and many IPs are discovered at the beginning of the epidemic.

Toxoplasma gondii, source to sea: higher contribution of domestic felids to terrestrial parasite loading despite lower infection prevalence.

Environmental transmission of Toxoplasma gondii, a global zoonotic parasite, adversely impacts human and animal health. Toxoplasma is a significant cause of mortality in threatened Southern sea otters, which serve as sentinels for disease threats to people and animals in coastal environments. As wild and domestic felids are the only recognized hosts capable of shedding Toxoplasma oocysts into the environment, otter infection suggests land-to-sea pathogen transmission. To assess relative contributions to terrestrial parasite loading, we evaluated infection and shedding among managed and unmanaged feral domestic cats, mountain lions, and bobcats in coastal California, USA. Infection prevalence differed among sympatric felids, with a significantly lower prevalence for managed feral cats (17%) than mountain lions, bobcats, or unmanaged feral cats subsisting on wild prey (73-81%). A geographic hotspot of infection in felids was identified near Monterey Bay, bordering a high-risk site for otter infection. Increased odds of oocyst shedding were detected in bobcats and unmanaged feral cats. Due to their large populations, pet and feral domestic cats likely contribute more oocysts to lands bordering the sea otter range than native wild felids. Continued coastal development may influence felid numbers and distribution, increase terrestrial pathogens in freshwater runoff, and alter disease dynamics at the human-animal-environment interface.

Spatial and temporal patterns of Leptospira infection in dogs from northern California: 67 cases (2001-2010).

OBJECTIVE: To conduct an epidemiological analysis of the spatial and temporal distribution of canine leptospirosis cases in northern California and detect spatial clustering in any region. DESIGN: Retrospective case-control study. ANIMALS: 67 dogs with leptospirosis and 271 control dogs. PROCEDURES: Medical records of case and control dogs were reviewed. Spatial coordinates of home addresses of the study population were analyzed visually and statistically via a Cuzick-Edwards test and spatial, temporal, and space-time permutation scan statistics. RESULTS: Cases were distributed around the San Francisco Bay region as well as in the Sierra Nevada foothills near Sacramento, Calif, whereas controls were principally distributed along route I-80 between San Francisco and Sacramento, Calif. Clustering was found for the second through sixth nearest neighboring cases via the global spatial cluster test. A local spatial cluster of 30 cases was identified in San Francisco (95% confidence interval, 1.3 to 7.0), and a temporal cluster of 18 cases was identified from May 2003 through May 2004 (95% confidence interval, 1.4 to 6.5). No significant space-time cluster was identified. CONCLUSIONS AND CLINICAL RELEVANCE: The use of geographic information systems provided a visual representation of the results of statistical analysis for the location and time at which leptospirosis cases occurred. This useful tool can be used to educate veterinary practitioners and the public about a potentially fatal zoonotic disease and direct vaccination strategies to help prevent disease occurrence.

Stochastic modelling of intra-household transmission of hepatitis C virus: evidence for substantial non-sexual infection.

OBJECTIVE: To simulate the probability of HCV transmission from an HCV seropositive index patient to susceptible household contacts through non-sexual exposures. METHODS: A modified Reed-Frost stochastic simulation model was used to assess the probability of HCV transmission from an HCV seropositive index patient to susceptible household contacts through non-sexual exposures. This mathematical model does not require the specification of infection onset times for individual, nor is it necessary to identify the chains of household infections. Therefore, this model can be used with serologic data on detected asymptomatic infections. The HCV serological data on 341 non-sexual household contacts of 86 HCV seropositive index patients were used in this simulation study. The frequency distribution of HCV infection of susceptibles for each household size of 4-8 initial susceptibles was calculated. A maximum likelihood procedure was used to estimate the non-sexual household transmission parameter for HCV infection for the range of household sizes studied and was used in 1000 stochastic iterations. The goodness-of-fit test was carried out to compare the observed proportions of households where HCV transmission occurred to one or more initial susceptible with mean expected simulated proportions of such households with varying sizes ranging from 4 to 8 initial susceptibles. RESULTS: The maximum likelihood estimates (90% probability interval (PI)) of binomial probability of HCV transmission within households with varying number of initial susceptible non-sexual household contacts ranged from 0.248 (90%PI: 0.031, 0.560) to 0.164 (90%PI: 0.011, 0.440) for household size of 4 and 8 respectively. The χ(2) goodness-of-fit test of observed and mean expected simulated proportions of households wherein at least one of the susceptibles was infected revealed good fit for households of all sizes examined (P ≥ 0.96). In a household, the probability of HCV transmission from the index HCV seropositive patient to susceptible via non-sexual contacts tended to decrease linearly as the household size increased from four to seven. CONCLUSION: Intra-household HCV transmission through non-sexual contacts may have substantial impact on HCV transmission and needs to be considered in an HCV control program.

Comparison of enzootic risk measures for predicting West Nile disease, Los Angeles, California, USA, 2004-2010.

In Los Angeles, California, USA, 2 epidemics of West Nile virus (WNV) disease have occurred since WNV was recognized in 2003. To assess which measure of risk was most predictive of human cases, we compared 3 measures: the California Mosquito-Borne Virus Surveillance and Response Plan Assessment, the vector index, and the Dynamic Continuous-Area Space-Time system. A case-crossover study was performed by using symptom onset dates from 384 persons with WNV infection to determine their relative environmental exposure to high-risk conditions as measured by each method. Receiver-operating characteristic plots determined thresholds for each model, and the area under the curve was used to compare methods. We found that the best risk assessment model for human WNV cases included surveillance data from avian, mosquito, and climate sources.

Assessing alternative low pathogenic avian influenza virus surveillance strategies in a live bird market.

Surveillance, comprised of sampling and testing, of low pathogenic avian influenza virus (LPAIV) in a live bird market (LBM) may enable the detection of the virus, reducing its spread within the market to humans and birds and to other markets within the LBM system. In addition, detection of infected birds would also reduce the probability of reassortment and possible change from a LPAIV to a highly pathogenic avian influenza virus, which would have a devastating impact on the economy, trade, and society. In this paper we present results from a computer simulation model based on previously collected survey and experimental transmission data. Once we validated the model with experimental transmission data, we applied it to address some of the questions that need to be answered in order to create an efficient surveillance system in an LBM. We have identified effective sampling times, patterns, and sizes that would enhance the probability of an early detection of LPAIV if present and minimize the associated labor and cost. The model may be modified to evaluate different sized and structured LBMs. It also provides the basis to evaluate an entire LBM system for the United States or other countries.

Spatio-temporal epidemiology of highly pathogenic avian influenza (H5N1) outbreaks in Nigeria, 2006-2008.

From 2006 to 2008, outbreaks of highly pathogenic avian influenza A (HPAI) virus of the H5N1 subtype occurred among poultry in Nigeria. We described the spatio-temporal patterns of the HPAI H5N1 outbreaks in Nigeria. Data of suspected and laboratory confirmed outbreaks maintained at the National Veterinary Research Institute Vom was analyzed using descriptive and exploratory analyses, GIS mapping, global and local spatial statistical analyses using the Cuzick-Edwards' (C-E) test and SaTScan Space-Time Scan Statistic. A total of 1654 suspected outbreaks were reported from 32 of the 36 States and the Federal Capital Territory (FCT), 299 were confirmed HPAI H5N1 positive from 27 states and FCT. The outbreaks occurred as three distinct epidemic waves with peak periods of January-March mainly in the North-West, North-Central and North-East regions during 2006 and 2007 and July-September in the South-West and South-South regions in 2007. Three spatio-temporal clusters were identified extending across States and international borders, consistent with disease transmission occurring through local and long-distance spread. This calls for enhanced strategies by the states and regional authorities to improve surveillance, prevention and control measures at the states, national and international levels.

Prevalence of low pathogenicity avian influenza virus during 2005 in two U.S. live bird market systems.

Oropharyngeal and cloacal swabs were collected from poultry sold in two live bird market (LBM) systems to estimate the prevalence of low pathogenicity avian influenza virus (LPAIV) shedding during the summer and fall of 2005. Random sampling was conducted in three LBMs in Minnesota where 50 birds were sampled twice weekly for 4 wk, and in three LBMs in a California marketing system. A stratified systematic sampling method was used to collect samples from Southern California LBMs, where LPAIV was detected during routine surveillance. No LPAIV was detected in the LBM system in Minnesota where realtime reverse transcription-PCR (RT-PCR) was conducted on oropharyngeal samples. RT-PCR was performed on swabs taken from 290 of 14,000, 65 of 252, and 60 of 211 birds at the three Southern California LBMs. The number of samples collected was based on the number of birds, age of the birds, and number of species present in the LBM. Virus isolation, subtyping, and sequencing of the hemagglutinin, neuraminidase, and other internal protein genes was performed on AIV-positive samples. The estimated prevalence of LPAIV in California was 0.345% in an LBM/supply farm with multiple ages of Japanese quail, 3% in an LBM with multiple ages and strains of chickens present, and 49.8% in an LBM with multiple species, multiple strains, and multiple ages. The positive virus samples were all LPAIV H6N2 and closely related to viruses isolated from Southern California in 2001 and 2004. Little or no comingling of poultry may contribute to little or no LPAIV detection in the LBMs.

Emergence and genetic variation of neuraminidase stalk deletions in avian influenza viruses.

When avian influenza viruses (AIVs) are transmitted from their reservoir hosts (wild waterfowl and shorebirds) to domestic bird species, they undergo genetic changes that have been linked to higher virulence and broader host range. Common genetic AIV modifications in viral proteins of poultry isolates are deletions in the stalk region of the neuraminidase (NA) and additions of glycosylation sites on the hemagglutinin (HA). Even though these NA deletion mutations occur in several AIV subtypes, they have not been analyzed comprehensively. In this study, 4,920 NA nucleotide sequences, 5,596 HA nucleotide and 4,702 HA amino acid sequences were analyzed to elucidate the widespread emergence of NA stalk deletions in gallinaceous hosts, the genetic polymorphism of the deletion patterns and association between the stalk deletions in NA and amino acid variants in HA. Forty-seven different NA stalk deletion patterns were identified in six NA subtypes, N1-N3 and N5-N7. An analysis that controlled for phylogenetic dependence due to shared ancestry showed that NA stalk deletions are statistically correlated with gallinaceous hosts and certain amino acid features on the HA protein. Those HA features included five glycosylation sites, one insertion and one deletion. The correlations between NA stalk deletions and HA features are HA-NA-subtype-specific. Our results demonstrate that stalk deletions in the NA proteins of AIV are relatively common. Understanding the NA stalk deletion and related HA features may be important for vaccine and drug development and could be useful in establishing effective early detection and warning systems for the poultry industry.

Epidemic and economic impacts of delayed detection of foot-and-mouth disease: a case study of a simulated outbreak in California.

The epidemic and economic impacts of Foot-and-mouth disease virus (FMDV) spread and control were examined by using epidemic simulation and economic (epinomic) optimization models. The simulated index herd was a ≥2,000 cow dairy located in California. Simulated disease spread was limited to California; however, economic impact was assessed throughout the United States and included international trade effects. Five index case detection delays were examined, which ranged from 7 to 22 days. The simulated median number of infected premises (IP) ranged from approximately 15 to 745, increasing as the detection delay increased from 7 to 22 days. Similarly, the median number of herds under quarantine increased from approximately 680 to 6,200, whereas animals slaughtered went from approximately 8,700 to 260,400 for detection delays of 7-22 days, respectively. The median economic impact of an FMD outbreak in California was estimated to result in national agriculture welfare losses of $2.3-$69.0 billion as detection delay increased from 7 to 22 days, respectively. If assuming a detection delay of 21 days, it was estimated that, for every additional hr of delay, the impact would be an additional approximately 2,000 animals slaughtered and an additional economic loss of $565 million. These findings underline the critical importance that the United States has an effective early detection system in place before an introduction of FMDV if it hopes to avoid dramatic losses to both livestock and the economy.