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

Occurrence of porcine reproductive and respiratory syndrome clinical outbreaks in Ontario sow herds, 2017 to 2019

Background

Porcine reproductive and respiratory syndrome (PRRS) is one of the important endemic diseases in swine populations. Monitoring PRRS frequency in commercial herd populations has often been based on laboratory submissions. However, a limitation of this approach is that new clinical outbreaks of PRRS are challenging to identify if epidemiological information is not provided. This hinders the estimation of basic measures such as incidence.

Objectives

The objectives of this study were to describe a system to monitor new clinical outbreaks in Ontario sow herds and to report the incidence of clinical PRRS outbreaks in a subset of Ontario sow herds.

Procedure

We compared herd-level outbreak data from January 1, 2017 to December 31, 2019. Cases were confirmed as positive based on observation of sow herds with typical clinical signs suggestive of PRRS, followed by laboratory confirmation of the PRRS virus.

Results and conclusion

The incidences from year to year were similar (P = 0.058) and were lower compared to estimates in the United States. Descriptively, the highest cumulative incidence was during 2018 (annual incidence risk = 0.067 cases per 100 sow herds, 95% CI = 0.050 to 0.090). This was characterized by an unusually high number of cases reported in the summer.

Sequence analysis of the GP5 protein of porcine reproductive and respiratory syndrome virus in Vietnam from 2007 to 2023

Introduction

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent 13 of porcine reproductive and respiratory syndrome (PRRS), which is one of the most economically 14 devastating viruses in the Vietnamese swine industry.

Methods

With a view toward determining the 15 genetic variation among PRRSV strains in Vietnam, we examined 271 PRRSV GP5 protein 16 sequences obtained from strains isolated in Vietnam from 2007 to 2023, for which we constructed 17 phylogenetic trees. Additionally, a collection of 52 PRRSV-1 strains and 80 PRRSV-2 strains 18 isolated in different years were specifically selected for nucleotide and amino acid homology analysis 19 and amino acid sequence alignment.

Results

The results revealed 76.1%-100.0% nucleotide and 20 75.2%-100.0% amino acid homologies for the PRRSV-1 GP5 gene, and 81.8%-100.0% nucleotide 21 and 81.1%-100.0% amino acid homologies for the PRRSV-2 GP5 gene. Amino acid mutation sites 22 in PRRSV-2 were found to be primarily distributed in the signal peptide region, antigenic sites, two 23 T-cell antigen regions, two highly variable regions (HVRs), and in the vicinity of the neutralizing 24 epitope, with a deletion mutation occurring in the neutralizing epitope, whereas amino acid mutations 25 in the PRRSV-1 sequences were found to occur predominantly in two T-cell epitopes. Genetic 26 analysis revealed that PRRSV-1 strains in Vietnam are of subtype 1 (Global), whereas PRRSV-2 27 strains are categorized into sublineages L1A, L5A, and L8E, with L8E being the predominantly 28 prevalent strain at present. Recombination analyses indicated that no significant recombination 29 events have occurred in any of the assessed 271 Vietnamese PRRSV strains.

Discussion

Our 30 analyses of 271 Vietnamese PRRSV strains have yielded valuable insights regarding the 31 epidemiological trends and genetic dynamics of PRRSV in Vietnam, and will provide a theoretical 32 basis for formulating prevention and control measures for PRRS and the development of PRRS 33 vaccines.

Spatial Epidemiology and Its Role in Prevention and Control of Swine Viral Disease

Spatial epidemiology offers a comprehensive framework for analyzing the spatial distribution and transmission of diseases, leveraging advanced technical tools and software, including Geographic Information Systems (GISs), remote sensing technology, statistical and mathematical software, and spatial analysis tools. Despite its increasing application to swine viral diseases (SVDs), certain challenges arise from its interdisciplinary nature. To support novices, frontline veterinarians, and public health policymakers in navigating its complexities, we provide a comprehensive overview of the common applications of spatial epidemiology in SVD. These applications are classified into four categories based on their objectives: visualizing and elucidating spatiotemporal distribution patterns, identifying risk factors, risk mapping, and tracing the spatiotemporal evolution of pathogens. We further elucidate the technical methods, software, and considerations necessary to accomplish these objectives. Additionally, we address critical issues such as the ecological fallacy and hypothesis generation in geographic correlation analysis. Finally, we explore the future prospects of spatial epidemiology in SVD within the One Health framework, offering a valuable reference for researchers engaged in the spatial analysis of SVD and other epidemics.

Assessing eco-geographic influences on COVID-19 transmission: a global analysis

COVID-19 has been massively transmitted for almost 3 years, and its multiple variants have caused serious health problems and an economic crisis. Our goal was to identify the influencing factors that reduce the threshold of disease transmission and to analyze the epidemiological patterns of COVID-19. This study served as an early assessment of the epidemiological characteristics of COVID-19 using the MaxEnt species distribution algorithm using the maximum entropy model. The transmission of COVID-19 was evaluated based on human factors and environmental variables, including climate, terrain and vegetation, along with COVID-19 daily confirmed case location data. The results of the SDM model indicate that population density was the major factor influencing the spread of COVID-19. Altitude, land cover and climatic factor showed low impact. We identified a set of practical, high-resolution, multi-factor-based maximum entropy ecological niche risk prediction systems to assess the transmission risk of the COVID-19 epidemic globally. This study provided a comprehensive analysis of various factors influencing the transmission of COVID-19, incorporating both human and environmental variables. These findings emphasize the role of different types of influencing variables in disease transmission, which could have implications for global health regulations and preparedness strategies for future outbreaks.

Contrasting PRRSV temporal lineage patterns at the individual farm, production system, and regional levels in Ohio and neighboring states from 2017 to 2021

Porcine reproductive and respiratory virus (PRRSV), one of the most significant viruses in the swine industry, has been challenging to control due to its high mutation and recombination rates and complexity. This retrospective study aimed to describe and compare the distribution of PRRSV lineages obtained at the individual farm, production system, and regional levels. PRRSV-2 (type 2) sequences (n = 482) identified between 2017 - 2021 were provided by a regional state laboratory (Ohio Department of Agriculture, Animal Disease Diagnostic Center (ODA-ADDL)) collected from swine farms in Ohio and neighboring states, including Indiana, Michigan, Pennsylvania, and West Virginia. Additional sequences (n = 138) were provided by one collaborating swine production system. The MUSCLE algorithm on Geneious Prime® was used to align the ORF5 region of PRRSV-2 sequences along with PRRSV live attenuated vaccine strains (n = 6) and lineage anchors (n = 169). Sequenced PRRSV-2 were assigned to the most identical lineage anchors/vaccine strains. Among all sequences (n = 620), 29.8% (185/620) were ≥ 98.0% identity with the vaccine strains, where 93.5% (173/185) and 6.5% (12/185) were identical with the L5 Ingelvac PRRS® MLV and L8 Fostera® PRRS vaccine strains, respectively, and excluded from the analysis. At the regional level across five years, the top five most identified lineages included L1A, L5, L1H, L1C, and L8. Among non-vaccine sequences with production system known, L1A sequences were mostly identified (64.3% - 100.0%) in five systems, followed by L1H (0.0% - 28.6%), L1C (0.0% - 10.5%), L5 (0.0% - 14.4%), L8 (0.0% - 1.3%), and L1F (0.0% - 0.5%). Furthermore, among non-vaccine sequences with the premise identification available (n = 262), the majority of sequences from five individual farms were either classified into L1A or L5. L1A and L5 sequences coexisted in three farms, while samples submitted by one farm contained L1A, L1H, and L5 sequences. Additionally, the lineage classification results of non-vaccine sequences were associated with their restriction fragment length polymorphism (RFLP) patterns (Fisher's exact test, p < 0.05). Overall, our results show that individual farm and production system-level PRRSV-2 lineage patterns do not necessarily correspond to regional-level patterns, highlighting the influence of individual farms and systems in shaping PRRSV occurrence within those levels, and highlighting the crucial goal of within-farm and system monitoring and early detection for accurate knowledge on PRRSV-2 lineage occurrence and emergence.

Spatiotemporal Distribution of PRRSV-1 Clades in Hungary with a Focus on the Era of Disease Eradication

Porcine reproductive and respiratory syndrome (PRRS) is the cause of the most severe economic losses in the pig industry worldwide. PRRSV is extremely diverse in Europe, which poses a significant challenge to disease control within a country or any region. With the combination of phylogenetic reconstruction and network analysis, we aimed to uncover the major routes of the dispersal of PRRSV clades within Hungary. In brief, by analyzing >2600 ORF5 sequences, we identified at least 12 clades (including 6 clades within lineage 1 and 3 clades within lineage 3) common in parts of Western Europe (including Denmark, Germany and the Netherlands) and identified 2 novel clades (designated X1 and X2). Of interest, some genetic clades unique to other central European countries, such as the Czech Republic and Poland, were not identified. The pattern of PRRSV clade distribution is consistent with the route of the pig trade among countries, showing that most of the identified clades were introduced from Western Europe when fatteners were transported to Hungary. As a result of rigorous implementation of the national eradication program, the swine population was declared officially free from PRRSV. This map of viral diversity and clade distribution will serve as valuable baseline information for the maintenance of PRRSV-free status in the post-eradication era.

Unveiling invisible farm-to-farm PRRSV-2 transmission links and routes through transmission tree and network analysis

The United States (U.S.) swine industry has struggled to control porcine reproductive and respiratory syndrome (PRRS) for decades, yet the causative virus, PRRSV-2, continues to circulate and rapidly diverges into new variants. In the swine industry, the farm is typically the epidemiological unit for monitoring, prevention, and control; breaking transmission among farms is a critical step in containing disease spread. Despite this, our understanding of farm transmission still is inadequate, precluding the development of tailored control strategies. Therefore, our objective was to infer farm-to-farm transmission links, estimate farm-level transmissibility as defined by reproduction numbers (R), and identify associated risk factors for transmission using PRRSV-2 open reading frame 5 (ORF5) gene sequences, animal movement records, and other data from farms in a swine-dense region of the U.S. from 2014 to 2017. Timed phylogenetic and transmission tree analyses were performed on three sets of sequences (n = 206) from 144 farms that represented the three largest genetic variants of the virus in the study area. The length of inferred pig-to-pig infection chains that corresponded to pairs of farms connected via direct animal movement was used as a threshold value for identifying other feasible transmission links between farms; these links were then transformed into farm-to-farm transmission networks and calculated farm-level R-values. The median farm-level R was one (IQR = 1-2), whereas the R value of 28% of farms was more than one. Exponential random graph models were then used to evaluate the influence of farm attributes and/or farm relationships on the occurrence of farm-to-farm transmission links. These models showed that, even though most transmission events cannot be directly explained by animal movement, movement was strongly associated with transmission. This study demonstrates how integrative techniques may improve disease traceability in a data-rich era by providing a clearer picture of regional disease transmission.

An assessment of enhanced biosecurity interventions and their impact on porcine reproductive and respiratory syndrome virus outbreaks within a managed group of farrow-to-wean farms, 2020-2021

Introduction

Porcine reproductive and respiratory syndrome virus (PRRSV) has been a challenge for the U.S. swine industry for over 30 years, costing producers more than $600 million annually through reproductive disease in sows and respiratory disease in growing pigs. In this study, the impact of enhanced biosecurity practices of site location, air filtration, and feed mitigation was assessed on farrow-to-wean sites managed by a large swine production management company in the Midwest United States. Those three factors varied in the system that otherwise had implemented a stringent biosecurity protocol on farrow-to-wean sites. The routine biosecurity followed commonplace activities for farrow-to-wean sites that included but were not limited to visitor registration, transport disinfection, shower-in/shower-out procedures, and decontamination and disinfection of delivered items and were audited.

Methods

Logistic regression was used to evaluate PRRSV infection by site based on the state where the site is located and air filtration use while controlling for other variables such as vaccine status, herd size, and pen vs. stall. A descriptive analysis was used to evaluate the impact of feed mitigation stratified by air filtration use.

Results

Sites that used feed mitigates as additives in the diets, air filtration of barns, and that were in less swine-dense areas appeared to experience fewer outbreaks associated with PRRSV infection. Specifically, 23.1% of farms that utilized a feed mitigation program experienced PRRSV outbreaks, in contrast to 100% of those that did not. Sites that did not use air filtration had 20 times greater odds of having a PRRSV outbreak. The strongest protective effect was found when both air filtration and feed mitigation were used. Locations outside of Minnesota and Iowa had 98.5-99% lesser odds of infection as well.

Discussion

Enhanced biosecurity practices may yield significant protective effects and should be considered for producers in swine-dense areas or when the site contains valuable genetics or many pigs.

Porcine Reproductive and Respiratory Syndrome (PRRS) Epidemiology in an Integrated Pig Company of Northern Italy: A Multilevel Threat Requiring Multilevel Interventions

Porcine reproductive and respiratory syndrome (PRRS) is probably the most relevant viral disease affecting pig farming. Despite the remarkable efforts paid in terms of vaccination administration and biosecurity, eradication and long-term control have often been frustrated. Unfortunately, few studies are currently available that objectively link, using a formal statistical approach, viral molecular epidemiology to the risk factors determining the observed scenario. The purpose of the present study is to contribute to filling this knowledge gap taking advantage of the advancements in the field of phylodynamics. Approximately one-thousand ORF7 sequences were obtained from strains collected between 2004 and 2021 from the largest Italian pig company, which implements strict compartmentalization among independent three-sites (i.e., sow herds, nurseries and finishing units) pig flows. The history and dynamics of the viral population and its evolution over time were reconstructed and linked to managerial choices. The viral fluxes within and among independent pig flows were evaluated, and the contribution of other integrated pig companies and rurally risen pigs in mediating such spreading was investigated. Moreover, viral circulation in Northern Italy was reconstructed using a continuous phylogeographic approach, and the impact of several environmental features on PRRSV strain persistence and spreading velocity was assessed. The results demonstrate that PRRSV epidemiology is shaped by a multitude of factors, including pig herd management (e.g., immunization strategy), implementation of strict-independent pig flows, and environmental features (e.g., climate, altitude, pig density, road density, etc.) among the others. Small farms and rurally raised animals also emerged as a potential threat for larger, integrated companies. These pieces of evidence suggest that none of the implemented measures can be considered effective alone, and a multidimensional approach, ranging from individual herd management to collaboration and information sharing among different companies, is mandatory for effective infection control.

A longitudinal study on PRRSV detection in swine herds with different demographics and PRRSV management strategies

Porcine reproductive and respiratory syndrome virus (PRRSV) has been one of the major health-related concerns in the swine production industry. Through its rapid transmission and mutation, the simultaneous circulation of multiple PRRSV strains can be a challenge in PRRSV diagnostic, control and surveillance. The objective of this longitudinal study was to describe the temporal detection of PRRSV in swine farms with different production types and PRRS management strategies. Tonsil scraping (n = 344) samples were collected from three breeding and two growing herds for approximately one year. In addition, processing fluids (n = 216) were obtained from piglet processing batches within the three breeding farms while pen-based oral fluids (n = 125) were collected in the two growing pig farms. Viral RNA extraction and reverse-transcription quantitative PCR (RT-qPCR) were conducted for all samples. The sample positivity threshold was set at quantification cycle (Cq) of ≤ 37. Statistical analyses were performed using generalized linear modelling and post hoc pairwise comparisons with Bonferroni adjustments using R statistical software. The results suggested a higher probability of detection in processing fluids compared to tonsil scraping specimens [odds ratio (OR) = 3.86; p = .096] in breeding farms whereas oral fluids were outperformed by tonsil scrapings (OR = 0.26; p < .01) in growing pig farms. The results described herein may lead to an improvement in PRRSV diagnostic and surveillance by selecting proper specimens.

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.

Phylogenetic Structure and Sequential Dominance of Sub-Lineages of PRRSV Type-2 Lineage 1 in the United States

The genetic diversity and frequent emergence of novel genetic variants of porcine reproductive and respiratory syndrome virus type-2 (PRRSV) hinders control efforts, yet drivers of macro-evolutionary patterns of PRRSV remain poorly documented. Utilizing a comprehensive database of >20,000 orf5 sequences, our objective was to classify variants according to the phylogenetic structure of PRRSV co-circulating in the U.S., quantify evolutionary dynamics of sub-lineage emergence, and describe potential antigenic differences among sub-lineages. We subdivided the most prevalent lineage (Lineage 1, accounting for approximately 60% of available sequences) into eight sub-lineages. Bayesian coalescent SkyGrid models were used to estimate each sub-lineage's effective population size over time. We show that a new sub-lineage emerged every 1 to 4 years and that the time between emergence and peak population size was 4.5 years on average (range: 2-8 years). A pattern of sequential dominance of different sub-lineages was identified, with a new dominant sub-lineage replacing its predecessor approximately every 3 years. Consensus amino acid sequences for each sub-lineage differed in key GP5 sites related to host immunity, suggesting that sub-lineage turnover may be linked to immune-mediated competition. This has important implications for understanding drivers of genetic diversity and emergence of new PRRSV variants in the U.S.

Development of a Dissemination Platform for Spatiotemporal and Phylogenetic Analysis of Avian Infectious Bronchitis Virus

Infecting large portions of the global poultry populations, the avian infectious bronchitis virus (IBV) remains a major economic burden in North America. With more than 30 serotypes globally distributed, Arkansas, Connecticut, Delaware, Georgia, and Massachusetts are among the most predominant serotypes in the United States. Even though vaccination is widely used, the high mutation rate exhibited by IBV is continuously triggering the emergence of new viral strains and hindering control and prevention measures. For that reason, targeted strategies based on constantly updated information on the IBV circulation are necessary. Here, we sampled IBV-infected farms from one US state and collected and analyzed 65 genetic sequences coming from three different lineages along with the immunization information of each sampled farm. Phylodynamic analyses showed that IBV dispersal velocity was 12.3 km/year. The majority of IBV infections appeared to have derived from the introduction of the Arkansas DPI serotype, and the Arkansas DPI and Georgia 13 were the predominant serotypes. When analyzed against IBV sequences collected across the United States and deposited in the GenBank database, the most likely viral origin of our sequences was from the states of Alabama, Georgia, and Delaware. Information about vaccination showed that the MILDVAC-MASS+ARK vaccine was applied on 26% of the farms. Using a publicly accessible open-source tool for real-time interactive tracking of pathogen spread and evolution, we analyzed the spatiotemporal spread of IBV and developed an online reporting dashboard. Overall, our work demonstrates how the combination of genetic and spatial information could be used to track the spread and evolution of poultry diseases, providing timely information to the industry. Our results could allow producers and veterinarians to monitor in near-real time the current IBV strain circulating, making it more informative, for example, in vaccination-related decisions.

Classification of porcine reproductive and respiratory syndrome virus in Ontario using Bayesian phylogenetics and assessment of temporal trends

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important swine viruses globally, including in Ontario, Canada. Understanding the evolution and relation of the various PRRSV genotypes in Ontario can provide insight into the epidemiology of the virus. The objectives of this study were to i) describe the variability of PRRSV genotypes in Ontario swine herds, and ii) evaluate possible groupings based on PRRSV genomic data. Virus open reading frame 5 (ORF-5) sequences collected from 2010 to 2018 were obtained from the Animal Health Laboratory, University of Guelph and Bayesian phylogenetic models were created from these. The PRRSV population of Ontario was then categorized into 10 distinct clades. Model comparisons indicated that the model with a constant population assumption fit the data best, which suggests that the net change in the PRRS virus variation of the entire population over the last decade was low. Nonetheless, viruses grouped into individual clades showed temporal clustering during distinct time intervals of the entire study period (P < 0.01).

Angiotensin II-mediated improvement of renal mitochondrial function via the AMPK/PGC-1α/NRF-2 pathway is superior to norepinephrine in a rat model of septic shock associated with acute renal injury

Background

This study sought to compare the therapeutic effects of angiotensin II (ANG II) and norepinephrine (NE) on cecal ligation and puncture (CLP)-induced septic acute kidney injury (AKI) in rats.

Methods

Sepsis shock was induced in anesthesia Sprague-Dawley male rats by CLP model for 24 hours. A total of 40 rats were divided into five groups, including control group, sham group, CLP group, CLP + ANG II group, and CLP + NE group. CLP + ANG II and CLP + NE group were administration of ANG II or NE after sepsis shock respectively, maintaining the MAP at 75–85 mmHg. CLP group was administration of saline for contrast. At 0, 18, 24 hours measured the renal blood grades and resistant index (RI) by ultrasound equipment. At 6, 12, 18 and 24 hours collected 0.5 mL blood sample for creatinine and lactic acid examination. Rats were observed for 24 hours after CLP procedure and then sacrificed for subsequent examination, rat serum were used to determine the levels of inflammatory response factors, kidney tissues were used to examine the oxidative stress factors and mitochondrial related proteins.” We added the sentence as following: “The AMPK, PGC-1α and NRF-2 expression in renal cortex was significantly increased in the CLP + ANG II group.

Results

Compared to the vehicle treatment, both ANG II and NE administration restored the decrease in the mean arterial pressure (MAP) and alleviated mitochondrial impairments in CLP rats. However, only ANG II alleviated CLP-induced abnormalities in serum creatinine and lactic acid concentrations, renal blood flow, the renal resistant index, renal histopathology, the production of proinflammatory cytokines, and oxidative stress markers in rats. ANG II was also found to be superior to NE in reversing the CLP-induced suppression of mitochondrial biogenesis-related protein expression in the kidneys of rats.

Conclusions

ANG II was better than NE in alleviating CLP-induced septic AKI in rats.

Ecological Niche Modeling: An Introduction for Veterinarians and Epidemiologists

Most infectious diseases in animals are not distributed randomly. Instead, diseases in livestock and wildlife are predictable in terms of the geography, time, and species affected. Ecological niche modeling approaches have been crucial to the advancement of our understanding of diversity and diseases distributions. This contribution is an introductory overview to the field of distributional ecology, with emphasis on its application for spatial epidemiology. A new, revised modeling framework is proposed for more detailed and replicable models that account for both the biology of the disease to be modeled and the uncertainty of the data available. Considering that most disease systems need at least two organisms interacting (i.e., host and pathogen), biotic interactions lie at the core of the pathogen's ecological niche. As a result, neglecting interacting organisms in pathogen dynamics (e.g., maintenance, reproduction, and transmission) may limit efforts to forecast disease distributions in veterinary epidemiology. Although limitations of ecological niche modeling are noted, it is clear that the application and value of ecological niche modeling to epidemiology will increase in the future. Potential research lines include the examination of the effects of biotic variables on model performance, assessments of protocols for model calibration in disease systems, and new tools and metrics for robust model evaluation. Epidemiologists aiming to employ ecological niche modeling theory and methods to reconstruct and forecast epidemics should familiarize themselves with ecological literature and must consider multidisciplinary collaborations including veterinarians to develop biologically sound, statistically robust analyses. This review attempts to increase the use of tools from ecology in disease mapping.

Spatial relative risk and factors associated with porcine reproductive and respiratory syndrome outbreaks in United States breeding herds

Details of incident cases of porcine reproductive and respiratory syndrome (PRRS) in United States breeding herds were obtained from the Morrison's Swine Health Monitoring Project. Herds were classified as cases if they reported an outbreak in a given season of the year and non-cases if they reported it in a season other than the case season or if they did not report a PRRS outbreak in any season. The geographic distribution of cases and non-cases was compared in each season of the year. The density of farms that had a PRRS outbreak during summer was higher in Southern Minnesota and Northwest-central Iowa compared to the density of the underlying population of non-case farms. This does not mean that PRRS outbreaks are more frequent during summer in absolute terms, but that there was a geographical clustering of herds breaking during summer in this area. Similar findings were observed in autumn. In addition, the density of farms reporting spring outbreaks was higher in the Southeast of the United States compared to that of the underlying population of non-case farms. A similar geographical clustering of PRRS outbreaks was observed during winter in the Southeast of the United States. Multivariable analyses, adjusting for the effect of known confounders, showed that the incidence rate of PRRS was significantly lower during winter and autumn during the porcine epidemic diarrhea (PED) epidemic years (2013-2014), compared to PRRS incidence rates observed during the winter and autumn of PED pre-epidemic years (2009-2012). After 2014, an increase in the incidence rate of PRRS was observed during winter and spring but not during autumn or summer. Pig dense areas were associated with a higher incidence rate throughout the year. However, this association tended to be stronger during the summer. Additionally, herds with ≥2500 sows had an increased incidence rate during all seasons except spring compared to those with <2500 sows. PRRS incidence was lower in year-round air-filtered herds compared to non-filtered herds throughout the year. We showed that not only the spatial risk of PRRS varies regionally according to the season of the year, but also that the effect of swine density, herd size and air filtering on PRRS incidence may also vary according to the season of the year. Further studies should investigate regional and seasonal drivers of disease. Breeding herds should maintain high biosecurity standards throughout the year.

Porcine reproductive and respiratory syndrome virus dissemination across pig production systems in the United States

Porcine reproductive and respiratory syndrome virus (PRRSV) remains widespread in the North American pig population. Despite improvements in virus characterization, it is unclear whether PRRSV infections are a product of viral circulation within production systems (local) or across production systems (external). Here, we examined the local and external dissemination dynamics of PRRSV and the processes facilitating its spread in three production systems. Overall, PRRSV genetic diversity has declined since 2018, while phylodynamic results support frequent external transmission. We found that PRRSV dissemination predominantly occurred mostly through transmission between farms of different production companies for several months, especially from November until May, a timeframe already established as PRRSV season. Although local PRRSV dissemination occurred mainly through regular pig flow (from sow to nursery and then to finisher farms), an important flux of PRRSV dissemination also occurred in the opposite direction, from finisher to sow and nursery farms, highlighting the importance of downstream farms as sources of the virus. Our results also showed that farms with pig densities of 500 to 1,000 pig/km² and farms located at a range within 0.5 km and 0.7 km from major roads were more likely to be infected by PRRSV, whereas farms at an elevation of 41 to 61 meters and surrounded by denser vegetation were less likely to be infected, indicating their role as dissemination barriers. In conclusion, our results demonstrate that external dissemination was intense, and reinforce the importance of farm proximity on PRRSV spread. Thus, consideration of farm location, geographic characteristics and animal densities across production systems may help to forecast PRRSV collateral dissemination.

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.

Prediction of seasonal patterns of porcine reproductive and respiratory syndrome virus RNA detection in the U.S. swine industry

We developed a model to predict the cyclic pattern of porcine reproductive and respiratory syndrome virus (PRRSV) RNA detection by reverse-transcription real-time PCR (RT-rtPCR) from 4 major swine-centric veterinary diagnostic laboratories (VDLs) in the United States and to use historical data to forecast the upcoming year's weekly percentage of positive submissions and issue outbreak signals when the pattern of detection was not as expected. Standardized submission data and test results were used. Historical data (2015-2017) composed of the weekly percentage of PCR-positive submissions were used to fit a cyclic robust regression model. The findings were used to forecast the expected weekly percentage of PCR-positive submissions, with a 95% confidence interval (CI), for 2018. During 2018, the proportion of PRRSV-positive submissions crossed 95% CI boundaries at week 2, 14-25, and 48. The relatively higher detection on week 2 and 48 were mostly from submissions containing samples from wean-to-market pigs, and for week 14-25 originated mostly from samples from adult/sow farms. There was a recurring yearly pattern of detection, wherein an increased proportion of PRRSV RNA detection in submissions originating from wean-to-finish farms was followed by increased detection in samples from adult/sow farms. Results from the model described herein confirm the seasonal cyclic pattern of PRRSV detection using test results consolidated from 4 VDLs. Wave crests occurred consistently during winter, and wave troughs occurred consistently during the summer months. Our model was able to correctly identify statistically significant outbreak signals in PRRSV RNA detection at 3 instances during 2018.

Evaluating an automated clustering approach in a perspective of ongoing surveillance of porcine reproductive and respiratory syndrome virus (PRRSV) field strains

Porcine reproductive and respiratory syndrome virus (PRRSV) has a major economic impact on the swine industry. The important genetic diversity needs to be considered for disease management. In this regard, information on the circulating endemic strains and their dispersal patterns through ongoing surveillance is beneficial. The objective of this project was to classify Quebec PRRSV ORF5 sequences in genetic clusters and evaluate stability of clustering results over a three-year period using an in-house automated clustering system. Phylogeny based on maximum likelihood (ML) was first inferred on 3661 sequences collected in 1998-2013 (Run 1). Then, sequences collected between January 2014 and September 2016 were sequentially added into 11 consecutive runs, each one covering a three-month period. For each run, detection of clusters, which were defined as groups of ≥15 sequences having a≥70% rapid bootstrap support (RBS) value, was automated in Python. Cluster stability was described for each cluster and run based on the number of sequences, RBS value, maximum pairwise distance and agreement in sequence assignment to a specific cluster. First and last run identified 29 and 33 clusters, respectively. In the last run, about 77% of the sequences were classified by the system. Most clusters were stable through time, with sequences attributed to one cluster in Run 1 staying in the same cluster for the 11 remaining runs. However, some initial groups were further subdivided into subgroups with time, which is important for monitoring since one specific wild-type cluster increased from 0% in 2007 to 45% of all sequences in 2016. This automated classification system will be integrated into ongoing surveillance activities, to facilitate communication and decision-making for stakeholders of the swine industry.

Seasonal patterns and space-time clustering of porcine reproductive and respiratory syndrome (PRRS) cases from 2008 to 2016 in Vietnam

Porcine reproductive and respiratory syndrome (PRRS) is an important disease in pig production and is endemic in Vietnam. No nationwide studies have been carried out to understand the spread of PRRS in Vietnam. The main objective of this study was to identify the seasonal patterns and space‐time clusters of PRRS from 2008 to 2016 using national surveillance data in Vietnam. A total of 614,219 cases were reported during the period. There was a seasonal pattern with single peak by region (except North Central Coast, showing double peaks in March and June). The seasonal plots from the Northern regions showed a higher peak between March and April, whereas the four regions from Southern part displayed a higher peak between June and August. Overall, outbreaks from the northern part of Vietnam tended to occur 3–4 months earlier than the southern part. When the spatial window was set at 50%, space‐time cluster analysis found that the first cluster occurred in the Red River Delta (RRD) (radius: 82.17 km; ratios: 5.5; period: Mar–May/2010) and the second (radius: 50.8 km; ratios: 10.61; period: Aug–Oct/2011) in the Mekong River Delta (MRD) region. Four other clusters were observed in the central and Southern parts. Our findings might provide better insight into the distribution of clusters and temporal patterns of PRRS in Vietnam. This study may provide policy makers with valuable information on the hotspot areas and timing of outbreaks. Also, it identifies when and where national control program could be implemented more efficiently by targeting resources for the prevention and control of PRRS.

Land Cover and Climate Change May Limit Invasiveness of Rhododendron ponticum in Wales

Invasive plant species represent a serious threat to biodiversity precipitating a sustained global effort to eradicate or at least control the spread of this phenomenon. Current distribution ranges of many invasive species are likely to be modified in the future by land cover and climate change. Thus, invasion management can be made more effective by forecasting the potential spread of invasive species. Rhododendron ponticum (L.) is an aggressive invasive species which appears well suited to western areas of the UK. We made use of MAXENT modeling environment to develop a current distribution model and to assess the likely effects of land cover and climatic conditions (LCCs) on the future distribution of this species in the Snowdonia National park in Wales. Six global circulation models (GCMs) and two representative concentration pathways (RCPs), together with a land cover simulation for 2050 were used to investigate species' response to future environmental conditions. Having considered a range of environmental variables as predictors and carried out the AICc-based model selection, we find that under all LCCs considered in this study, the range of R. ponticum in Wales is likely to contract in the future. Land cover and topographic variables were found to be the most important predictors of the distribution of R. ponticum. This information, together with maps indicating future distribution trends will aid the development of mitigation practices to control R. ponticum.

Emergence of canine parvovirus subtype 2b (CPV-2b) infections in Australian dogs

Tracing the temporal dynamics of pathogens is crucial for developing strategies to detect and limit disease emergence. Canine parvovirus (CPV-2) is an enteric virus causing morbidity and mortality in dogs around the globe. Previous work in Australia reported that the majority of cases were associated with the CPV-2a subtype, an unexpected finding since CPV-2a was rapidly replaced by another subtype (CPV-2b) in many countries. Using a nine-year dataset of CPV-2 infections from 396 dogs sampled across Australia, we assessed the population dynamics and molecular epidemiology of circulating CPV-2 subtypes. Bayesian phylogenetic Skygrid models and logistic regressions were used to trace the temporal dynamics of CPV-2 infections in dogs sampled from 2007 to 2016. Phylogenetic models indicated that CPV-2a likely emerged in Australia between 1973 and 1988, while CPV-2b likely emerged between 1985 and 1998. Sequences from both subtypes were found in dogs across continental Australia and Tasmania, with no apparent effect of climate variability on subtype occurrence. Both variant subtypes exhibited a classical disease emergence pattern of relatively high rates of evolution during early emergence followed by subsequent decreases in evolutionary rates over time. However, the CPV-2b subtype maintained higher mutation rates than CPV-2a and continued to expand, resulting in an increase in the probability that dogs will carry this subtype over time. Ongoing monitoring programs that provide molecular epidemiology surveillance will be necessary to detect emergence of new variants and make informed recommendations to develop reliable detection and vaccine methods.