The population genetics of the causative agent of snake fungal disease indicate recent introductions to the USA.

Snake fungal disease (SFD; ophidiomycosis), caused by the pathogen Ophidiomyces ophiodiicola (Oo), has been documented in wild snakes in North America and Eurasia, and is considered an emerging disease in the eastern United States of America. However, a lack of historical disease data has made it challenging to determine whether Oo is a recent arrival to the USA or whether SFD emergence is due to other factors. Here, we examined the genomes of 82 Oo strains to determine the pathogen's history in the eastern USA. Oo strains from the USA formed a clade (Clade II) distinct from European strains (Clade I), and molecular dating indicated that these clades diverged too recently (approximately 2,000 years ago) for transcontinental dispersal of Oo to have occurred via natural snake movements across Beringia. A lack of nonrecombinant intermediates between clonal lineages in Clade II indicates that Oo has actually been introduced multiple times to North America from an unsampled source population, and molecular dating indicates that several of these introductions occurred within the last few hundred years. Molecular dating also indicated that the most common Clade II clonal lineages have expanded recently in the USA, with time of most recent common ancestor mean estimates ranging from 1985 to 2007 CE. The presence of Clade II in captive snakes worldwide demonstrates a potential mechanism of introduction and highlights that additional incursions are likely unless action is taken to reduce the risk of pathogen translocation and spillover into wild snake populations.

Broad-Scale Assessment of Methylmercury in Adult Amphibians.

Mercury (Hg) is a toxic contaminant that has been mobilized and distributed worldwide and is a threat to many wildlife species. Amphibians are facing unprecedented global declines due to many threats including contaminants. While the biphasic life history of many amphibians creates a potential nexus for methylmercury (MeHg) exposure in aquatic habitats and subsequent health effects, the broad-scale distribution of MeHg exposure in amphibians remains unknown. We used nonlethal sampling to assess MeHg bioaccumulation in 3,241 juvenile and adult amphibians during 2017-2021. We sampled 26 populations (14 species) across 11 states in the United States, including several imperiled species that could not have been sampled by traditional lethal methods. We examined whether life history traits of species and whether the concentration of total mercury in sediment or dragonflies could be used as indicators of MeHg bioaccumulation in amphibians. Methylmercury contamination was widespread, with a 33-fold difference in concentrations across sites. Variation among years and clustered subsites was less than variation across sites. Life history characteristics such as size, sex, and whether the amphibian was a frog, toad, newt, or other salamander were the factors most strongly associated with bioaccumulation. Total Hg in dragonflies was a reliable indicator of bioaccumulation of MeHg in amphibians (R2 ≥ 0.67), whereas total Hg in sediment was not (R2 ≤ 0.04). Our study, the largest broad-scale assessment of MeHg bioaccumulation in amphibians, highlights methodological advances that allow for nonlethal sampling of rare species and reveals immense variation among species, life histories, and sites. Our findings can help identify sensitive populations and provide environmentally relevant concentrations for future studies to better quantify the potential threats of MeHg to amphibians.

Avian influenza virus prevalence in marine birds is dependent on ocean temperatures.

Waterfowl and shorebirds are the primary hosts of influenza A virus (IAV), however, in most surveillance efforts, large populations of birds are not routinely examined; specifically marine ducks and other birds that reside predominately on or near the ocean. We conducted a long-term study sampling sea ducks and gulls in coastal Maine for IAV and found a virus prevalence (1.7%) much lower than is typically found in freshwater duck populations. We found wide year-to-year variation in virus detection in sea ducks and that the ocean water temperature was an important factor affecting IAV prevalence. In particular, the ocean temperature that occurred 11 d prior to collecting virus positive samples was important while water temperature measured concurrently with host sampling had no explanatory power for viral detection. We also experimentally showed that IAV is relatively unstable in sea water at temperatures typically found during our sampling. This represents the first report of virus prevalence and actual environmental data that help explain the variation in marine IAV transmission dynamics.

Pathology and Case Definition of Severe Perkinsea Infection of Frogs.

Severe Perkinsea infection (SPI) is an emerging disease of frogs responsible for mass mortalities of tadpoles across the United States. It is caused by protozoa belonging to the phylum Perkinsozoa that form a distinct group referred to as the Pathogenic Perkinsea Clade of frogs. In this work, we provide detailed description of gross and histologic lesions from 178 naturally infected tadpoles, including 10 species from 22 mortality events and 6 amphibian health monitoring studies from diverse geographic areas. On external examination, we observed abdominal distension (10, 5.6%), cutaneous erythema and petechia (3, 1.7%), subcutaneous edema (3, 1.7%), and areas of white skin discoloration (3, 1.7%). On macroscopic examination of internal organs, we found hepatomegaly (68, 38.2%), splenomegaly (51, 28.7%), nephromegaly (47, 26.4%), ascites (15, 8.4%), segmental irregular thickening and white discoloration of the intestine (8, 4.5%), pancreatomegaly (4, 2.2%), and pancreatic petechia (1, 0.6%). Histologically, over 60% of the liver (148/165, 89.7%), kidney (113/147, 76.9%), spleen (96/97, 99%), and pancreas (46/68, 67.6%) were invaded by myriad intracellular and extracellular Perkinsea hypnospore-like and trophozoite-like organisms. Numerous other tissues were affected to a lesser extent. Mild histiocytic inflammation with fewer lymphocytes or eosinophils was commonly observed in areas of infection that were not obscured by lympho-granulocytic hematopoietic tissue. In light of these observations, we suggest a logical pathogenesis sequence. Finally, we propose a "case definition" for SPI to promote standardized communication of results and prevent misdiagnosis with epidemiological and pathologically overlapping diseases such as ranavirosis.

Surveillance for Highly Pathogenic Avian Influenza Virus in Wild Birds during Outbreaks in Domestic Poultry, Minnesota, 2015.

In 2015, a major outbreak of highly pathogenic avian influenza virus (HPAIV) infection devastated poultry facilities in Minnesota, USA. To understand the potential role of wild birds, we tested 3,139 waterfowl fecal samples and 104 sick and dead birds during March 9-June 4, 2015. HPAIV was isolated from a Cooper's hawk but not from waterfowl fecal samples.

Morbidity in California giant salamander (Dicamptodon ensatus Eschscholtz, 1833) caused by Euryhelmis sp. Poche, 1926 (Trematoda: Heterophyiidae).

In the fall of 2021, California Department of Fish and Wildlife reported larval and adult California giant salamanders (Dicamptodon ensatus Eschscholtz, 1833) with skin lesions at multiple creeks in Santa Clara and Santa Cruz Counties, California, USA. Field signs in both stages included rough, lumpy textured skin, and larvae with tails that were disproportionately long, flat, wavy, and flaccid. Presence of large-bodied larvae suggested delayed metamorphosis, with some larvae having cloudy eyes and suspected blindness. To determine the cause of the disease, three first-of-the-year salamanders from one location were collected, euthanized with 20% benzocaine, and submitted for necropsy to the U.S. Geological Survey, National Wildlife Health Center. Upon gross examination, all salamanders were emaciated with no internal fat stores, and had multiple pinpoint to 1.5-mm diameter raised nodules in the skin over the body, including the head, gills, dorsum, ventrum, all four limbs, and the tail; one also had nodules in the oral cavity and tongue. Histologically all salamanders had multiple encysted metacercariae in the dermis, subcutis, and skeletal muscles of the head, body, and tail that were often associated with granulomatous and granulocytic inflammation and edema. A small number of encysted metacercariae or empty cysts were present in the gills with minimal inflammation, and rarely in the kidney with no associated inflammation. Morphology of live metacercariae (Trematoda: Heterophyiidae), and sequencing of the 28S rRNA gene identified a species of Euryhelmis (Poche, 1926). Artificial digestion of a 1.65 g, decapitated, eviscerated carcass yielded 773 metacercariae, all of similar size and morphology as the live specimens. Based on these findings, the poor body condition of these salamanders was concluded to be due to heavy parasite burden. Environmental factors such as drought, increased temperature, and overcrowded conditions may be exacerbating parasite infections in these populations of salamander.

Network transmission inference: host behavior and parasite life cycle make social networks meaningful in disease ecology.

The process of disease transmission is determined by the interaction of host susceptibility and exposure to parasite infectious stages. Host behavior is an important determinant of the likelihood of exposure to infectious stages but is difficult to measure and often assumed to be homogenous in models of disease spread. We evaluated the importance of precisely defining host contact when using networks that estimate exposure and predict infection prevalence in a replicated, empirical system. In particular, we hypothesized that infection patterns would be predicted only by a contact network that is defined according to host behavior and parasite life cycle. Two competing host contact criteria were used to construct networks defined by parasite life cycle and social contacts. First, parasite-defined contacts were based on shared space with a time delay corresponding to the environmental development time of nematode parasites with a direct fecal-oral life cycle. Second, social contacts were defined by shared space in the same time period. To quantify the competing networks of exposure and infection, we sampled natural populations of the eastern chipmunk (Tamias striatus) and infection of their gastrointestinal helminth community using replicated longitudinal capture-mark-recapture techniques. We predicted that (1) infection with parasites with direct fecal-oral life cycles would be explained by the time delay contact network, but not the social contact network; (2) infection with parasites with trophic life cycles (via a mobile intermediate host; thus, spatially decoupling transmission from host contact) would not be explained by either contact network. The prevalence of fecal-oral life cycle nematode parasites was strongly correlated to the number and strength of network connections from the parasite-defined network (including the time delay), while the prevalence of trophic life cycle parasites was not correlated with any network metrics. We concluded that incorporating the parasite life cycle, relative to the way that exposure is measured, is key to inferring transmission and can be empirically quantified using network techniques. In addition, appropriately defining and measuring contacts according the life history of the parasite and relevant behaviors of the host is a crucial step in applying network analyses to empirical systems.

Epistylis spp. Infestation in Two Species of Mud Turtles (Kinosternon spp.) in the American Southwest.

The protistan genus Epistylis contains freshwater colonial species that attach to aquatic organisms in an epibiotic or parasitic relationship. They are known to attach to the epidermis and shells of aquatic turtles, but have not been reported to cause heavy infestations or morbidity in turtles. We documented heavy infestations of Epistylis spp. in several populations of Sonoran mud turtles (Kinosternon sonoriense) inhabiting livestock ponds in Arizona, USA, and rough-footed mud turtles (Kinosternon hirtipes) from livestock ponds in Texas, USA, over the course of several years. Severe Epistylis spp. infestations on mud turtles appeared to alter diving and swimming behavior when compared to uninfested conspecifics. Infestations were cleared in captivity using tap water or a 10% salt solution, and the turtles had no permanent damage to their shell or epidermis upon clearing. While several of the mud turtles we observed had poor body condition, it is possible that the severe infestations we observed were caused by a comorbidity associated with a pathogen, parasite, or poor habitat quality that made the turtles more susceptible to the Epistylis spp. infestation. Further research on causes for these severe infestations are warranted because they contribute to changes in behavior of the heavily infested turtles and may contribute to morbidity in Kinosternon spp. when mud turtles inhabit extremely warm, shallow, eutrophic aquatic habitats, such as livestock ponds.

KEEPING THE HEAT ON: WEIGHTED SURVEILLANCE FOR CHYTRID FUNGUS (BATRACHOCHYTRIUM DENDROBATIDIS) IN DIXIE VALLEY TOADS (ANAXYRUS [= BUFO] WILLIAMSI).

Introduced fungal pathogens have caused declines and extinctions of naïve wildlife populations across vertebrate classes. Consequences of introduced pathogens to hosts with small ranges might be especially severe because of limited redundancy to rescue populations and lower abundance that may limit the resilience of populations to perturbations like disease introduction. As a complement to biosecurity measures to prevent the spread of pathogens, surveillance programs may enable early detection of pathogens, when management actions to limit the effects of pathogens on naïve hosts might be most beneficial. We analyzed surveillance data for the endangered and narrowly endemic Dixie Valley toad (Anaxyrus [= Bufo] williamsi) from two time periods (2011-2014 and 2019-2021) to estimate the minimum detectable prevalence of the amphibian fungal pathogen Batrachochytrium dendrobatidis (Bd). We assessed if detection efficiency could be improved by using samples from both Dixie Valley toads and co-occurring introduced American bullfrogs (Lithobates catesbeianus) and literature-derived surveillance weights. We further evaluated a weighted surveillance design to increase the efficiency of surveillance efforts for Bd within the toad's small (<6 km2) range. We found that monitoring adult and larval American bullfrogs would probably detect Bd more efficiently than monitoring Dixie Valley toads alone. Given that no Bd was detected, minimum detectable prevalence of Bd was <3% in 2011-2014, and <5% (Dixie Valley toads only) and <10% (American bullfrogs only) in 2019-2021. Optimal management for Bd depends on the mechanisms underlying its apparent absence from the range of Dixie Valley toads, but a balanced surveillance scheme that includes sampling American bullfrogs to increase the likelihood of detecting Bd, and adult Dixie Valley toads to ensure broad spatial coverage where American bullfrogs do not occur, would probably result in efficient surveillance, which might permit timely management of Bd if it is detected.

Paranannizziopsis spp. infections in wild snakes and a qPCR assay for detection of the fungus.

The emergence of ophidiomycosis (or snake fungal disease) in snakes has prompted increased awareness of the potential effects of fungal infections on wild reptile populations. Yet, aside from Ophidiomyces ophidiicola, little is known about other mycoses affecting wild reptiles. The closely related genus Paranannizziopsis has been associated with dermatomycosis in snakes and tuataras in captive collections, and P. australasiensis was recently identified as the cause of skin infections in non-native wild panther chameleons (Furcifer pardalis) in Florida, USA. Here we describe five cases of Paranannizziopsis spp. associated with skin lesions in wild snakes in North America and one additional case from a captive snake from Connecticut, USA. In addition to demonstrating that wild Nearctic snakes can serve as a host for these fungi, we also provide evidence that the genus Paranannizziopsis is widespread in wild snakes, with cases being identified in Louisiana (USA), Minnesota (USA), Virginia (USA), and British Columbia (Canada). Phylogenetic analyses conducted on multiple loci of the fungal strains we isolated identified P. australasiensis in Louisiana and Virginia; the remaining strains from Minnesota and British Columbia did not cluster with any of the described species of Paranannizziopsis, although the strains from British Columbia appear to represent a single lineage. Finally, we designed a pan-Paranannizziopsis real-time PCR assay targeting the internal transcribed spacer region 2. This assay successfully detected DNA of all described species of Paranannizziopsis and the two potentially novel taxa isolated in this study and did not cross-react with closely related fungi or other fungi commonly found on the skin of snakes. The assay was 100% sensitive and specific when screening clinical (skin tissue or skin swab) samples, although full determination of the assay's performance will require additional follow up due to the small number of clinical samples (n = 14 from 11 snakes) available for testing in our study. Nonetheless, the PCR assay can provide an important tool in further investigating the prevalence, distribution, and host range of Paranannizziopsis spp. and facilitate more rapid diagnosis of Paranannizziopsis spp. infections that are otherwise difficult to differentiate from other dermatomycoses.

The dynamics of macroparasite host-self-infection: a study of the patterns and processes of pinworm (Oxyuridae) aggregation.

OBJECTIVES: Among parasites, Taylor's power law identifies a tight relationship in aggregation of macroparasite infection intensity with few exceptions; notably, the nematode family Oxyuridae tends to have higher than expected aggregation. Oxyuridae infect a wide range of mammalian hosts and have a unique reproductive strategy that involves conventional horizontal transmission, as well as re-infection of an already infected host. We asked the question, do the unique aspects of pinworm life-history explain an exception to the widely observed patterns of aggregation of parasite populations? METHODS: We empirically examined the differences among Oxyuridae (genus: Syphacia) compared with other helminth (genus: Heligmosomoides) parasite aggregations in 2 rodent hosts with similar ecology: the yellow-necked mouse (Apodemus flavicollis) from Trento, Italy and the white-footed mouse (Peromyscus leucopus) from Pennsylvania, USA. To investigate the effects of pinworm life-history characteristics on generating aggregation, we present a stochastic model that explores aggregation under a range of host-self-infection, parasite death, and transmission scenarios. RESULTS: Oxyuridae parasites had consistently greater aggregation compared to other nematodes regardless of host or parasite species identity, and pinworm aggregation exceeded the range of macroparasite aggregation described previously. CONCLUSIONS: Our simulations demonstrate that host-self-infection, on its own, is sufficient to generate aggregation values greater than the predicted values.

Diversity and distribution of white-tailed deer mtDNA lineages in chronic wasting disease (CWD) outbreak areas in southern Wisconsin, USA.

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy affecting North American cervids. Because it is uniformly fatal, the disease is a major concern in the management of white-tailed deer populations. Management programs to control CWD require improved knowledge of deer interaction, movement, and population connectivity that could influence disease transmission and spread. Genetic methods were employed to evaluate connectivity among populations in the CWD management zone of southern Wisconsin. A 576-base-pair region of the mitochondrial DNA of 359 white-tailed deer from 12 sample populations was analyzed. Fifty-eight variable sites were detected within the sequence, defining 43 haplotypes. While most sample populations displayed similar levels of haplotype diversity, individual haplotypes were clustered on the landscape. Spatial clusters of different haplotypes were apparent in distinct ecoregions surrounding CWD outbreak areas. The spatial distribution of mtDNA haplotypes suggests that clustering of the deer matrilineal groups and population connectivity are associated with broad-scale geographic landscape features. These landscape characteristics may also influence the contact rates between groups and therefore the potential spread of CWD; this may be especially true of local disease spread between female social groups. Our results suggest that optimal CWD management needs to be tailored to fit gender-specific dispersal behaviors and regional differences in deer population connectivity. This information will help wildlife managers design surveillance and monitoring efforts based on population interactions and potential deer movement among CWD-affected and unaffected areas.

Acute mortality in California tiger salamander (Ambystoma californiense) and Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum) caused by Ribeiroia ondatrae (Class: Trematoda).

In early September 2019, a morbidity and mortality event affecting California tiger salamanders (Ambystoma californiense) and Santa Cruz long-toed salamanders (Ambystoma macrodactylum croceum) in late stages of metamorphosis was reported at a National Wildlife Refuge in Santa Cruz County, California, U.S.A. During the postmortem disease investigation, severe integumentary metacercarial (Class: Trematoda) infection, associated with widespread skin lesions, was observed. Planorbid snails collected from the ponds of the refuge within seven days of the mortality event were infected with Ribeiroia ondatrae, a digenetic trematode that can cause malformation and death in some amphibians. We suggest sustained seasonal high-water levels due to active habitat management along with several years of increased rainfall led to increased bird visitation, increased over-wintering of snails, and prolonged salamander metamorphosis, resulting in a confluence of conditions and cascading of host-parasite dynamics to create a hyper-parasitized state.

Highly pathogenic avian influenza virus H5N2 (clade 2.3.4.4) challenge of mallards age appropriate to the 2015 midwestern poultry outbreak.

BACKGROUND: The 2015 highly pathogenic avian influenza virus (HPAIV) H5N2 clade 2.3.4.4 outbreak in upper midwestern U.S. poultry operations was not detected in wild birds to any great degree during the outbreak, despite wild waterfowl being implicated in the introduction, reassortment, and movement of the virus into North America from Asia. This outbreak led to the demise of over 50 million domestic birds and occurred mainly during the northward spring migration of adult avian populations. OBJECTIVES: There have been no experimental examinations of the pathogenesis, transmission, and population impacts of this virus in adult wild waterfowl with varying exposure histories-the most relevant age class. METHODS: We captured, housed, and challenged adult wild mallards (Anas platyrhynchos) with HPAIV H5N2 clade 2.3.4.4 and measured viral infection, viral excretion, and transmission to other mallards. RESULTS: All inoculated birds became infected and excreted moderate amounts of virus, primarily orally, for up to 14 days. Cohoused, uninoculated birds also all became infected. Serological status had no effect on susceptibility. There were no obvious clinical signs of disease, and all birds survived to the end of the study (14 days). CONCLUSIONS: Based on these results, adult mallards are viable hosts of HPAIV H5N2 regardless of prior exposure history and are capable of transporting the virus over short and long distances. These findings have implications for surveillance efforts. The capture and sampling of wild waterfowl in the spring, when most surveillance programs are not operating, are important to consider in the design of future HPAIV surveillance programs.

The ecology of chronic wasting disease in wildlife.

Prions are misfolded infectious proteins responsible for a group of fatal neurodegenerative diseases termed transmissible spongiform encephalopathy or prion diseases. Chronic Wasting Disease (CWD) is the prion disease with the highest spillover potential, affecting at least seven Cervidae (deer) species. The zoonotic potential of CWD is inconclusive and cannot be ruled out. A risk of infection for other domestic and wildlife species is also plausible. Here, we review the current status of the knowledge with respect to CWD ecology in wildlife. Our current understanding of the geographic distribution of CWD lacks spatial and temporal detail, does not consider the biogeography of infectious diseases, and is largely biased by sampling based on hunters' cooperation and funding available for each region. Limitations of the methods used for data collection suggest that the extent and prevalence of CWD in wildlife is underestimated. If the zoonotic potential of CWD is confirmed in the short term, as suggested by recent results obtained in experimental animal models, there will be limited accurate epidemiological data to inform public health. Research gaps in CWD prion ecology include the need to identify specific biological characteristics of potential CWD reservoir species that better explain susceptibility to spillover, landscape and climate configurations that are suitable for CWD transmission, and the magnitude of sampling bias in our current understanding of CWD distribution and risk. Addressing these research gaps will help anticipate novel areas and species where CWD spillover is expected, which will inform control strategies. From an ecological perspective, control strategies could include assessing restoration of natural predators of CWD reservoirs, ultrasensitive CWD detection in biotic and abiotic reservoirs, and deer density and landscape modification to reduce CWD spread and prevalence.

Batrachochytrium salamandrivorans (Bsal) not detected in an intensive survey of wild North American amphibians.

The salamander chytrid fungus (Batrachochytrium salamandrivorans [Bsal]) is causing massive mortality of salamanders in Europe. The potential for spread via international trade into North America and the high diversity of salamanders has catalyzed concern about Bsal in the U.S. Surveillance programs for invading pathogens must initially meet challenges that include low rates of occurrence on the landscape, low prevalence at a site, and imperfect detection of the diagnostic tests. We implemented a large-scale survey to determine if Bsal was present in North America designed to target taxa and localities where Bsal was determined highest risk to be present based on species susceptibility and geography. Our analysis included a Bayesian model to estimate the probability of occurrence of Bsal given our prior knowledge of the occurrence and prevalence of the pathogen. We failed to detect Bsal in any of 11,189 samples from 594 sites in 223 counties within 35 U.S. states and one site in Mexico. Our modeling indicates that Bsal is highly unlikely to occur within wild amphibians in the U.S. and suggests that the best proactive response is to continue mitigation efforts against the introduction and establishment of the disease and to develop plans to reduce impacts should Bsal establish.

Does elevated testosterone result in increased exposure and transmission of parasites?

Male-biased infection is a common phenomenon in vertebrate-parasite systems and male-biased transmission has been experimentally demonstrated. One mechanism that is hypothesized to create male-biased transmission is the immuno-suppressive effect of testosterone because it increases susceptibility to infection. Testosterone also influences host behaviour and, consequently, may increase exposure to parasites. To test how testosterone could increase exposure and transmission, we undertook a longitudinal mark-recapture study where we experimentally elevated testosterone levels in wild male rodents. Individuals in control populations reduced the average number of contacts over the treatment period, while populations with experimentally elevated testosterone levels maintained the number of contacts between hosts. As a result, the transmission potential was higher in testosterone treated populations compared to controls. Our results indicated that males with high-testosterone levels alter the population-level contacts, producing different social networks and increasing transmission potential compared to those where testosterone is at background levels.

Mortality due to Tyzzer's Disease of Muskrats (Ondatra zibethicus) in Northern Ohio, USA.

In 2017, we investigated a mortality event of muskrat (Ondatra zibethicus) in northwest Ohio, US, and determined the causes of death to be from Tyzzer's disease due to Clostridium piliforme and Klebsiella pneumoniae septicemia. The gross presentation resembled tularemia, which highlighted the importance of a complete diagnostic investigation.

Estimating and exploring the proportions of inter- and intrastate cattle shipments in the United States.

Mathematical models are key tools for the development of surveillance, preparedness and response plans for the potential events of emerging and introduced foreign animal diseases. Creating these types of plans requires data; when data are incomplete, mathematical models can help fill in missing information, provided they are informed by the data that are available. In the United States, the most complete national-scale data available on cattle shipments are based on Interstate Certificates of Veterinary Inspection, which track the shipment of cattle between states; data on intrastate cattle shipments are lacking. Here we develop four new datasets on intrastate cattle shipments in the U.S., including an expert elicitation survey covering 19 states and territories and three state-level brand inspection data sets. The expert elicitation survey provides estimates on the proportion of shipments that travel interstate over multiple regions of the U.S. These survey data also identify differences in shipment patterns between regions, cattle commodity types, and sectors of the cattle industry. These survey data cover more states than any other source of intrastate data; however, one limitation of these data is the small number of participating experts in many of the states, only seven of the 19 responding states and territories had a group size of three or larger. The brand data sets include origin and destination information for both intra- and interstate shipments. These data, therefore, also provide detailed information on the proportion of interstate shipments in three Western states, including the temporal and geographic variation in shipments. Because the survey and brand data overlap in the Western U.S., they can be compared. We find that in the Western U.S. the expert estimates of the overall proportion of cattle shipments matched the brand data well. However, the experts estimated that there would be larger differences in beef and dairy shipments than the brand data show. This suggests the cattle industries in the West may be sending similar proportions of commodity specific cattle shipments over state lines. We additionally used the expert survey data to explore how differences in the proportion of interstate shipments can change predictions about cattle shipment patterns using the example of model-guided suggestions for targeted surveillance in Texas. Together these four data sets are the most extensive and geographically comprehensive information to date on intrastate cattle shipments. Additionally, our analyses on predicted shipment patterns suggest that assumptions about intrastate shipments could have consequences for targeted surveillance.

Inferring epidemiologic dynamics from viral evolution: 2014-2015 Eurasian/North American highly pathogenic avian influenza viruses exceed transmission threshold, R0 = 1, in wild birds and poultry in North America.

Highly pathogenic avian influenza virus (HPAIV) is a multihost pathogen with lineages that pose health risks for domestic birds, wild birds, and humans. One mechanism of intercontinental HPAIV spread is through wild bird reservoirs, and wild birds were the likely sources of a Eurasian (EA) lineage HPAIV into North America in 2014. The introduction resulted in several reassortment events with North American (NA) lineage low-pathogenic avian influenza viruses and the reassortant EA/NA H5N2 went on to cause one of the largest HPAIV poultry outbreaks in North America. We evaluated three hypotheses about novel HPAIV introduced into wild and domestic bird hosts: (i) transmission of novel HPAIVs in wild birds was restricted by mechanisms associated with highly pathogenic phenotypes; (ii) the HPAIV poultry outbreak was not self-sustaining and required viral input from wild birds; and (iii) reassortment of the EA H5N8 generated reassortant EA/NA AIVs with a fitness advantage over fully Eurasian lineages in North American wild birds. We used a time-rooted phylodynamic model that explicitly incorporated viral population dynamics with evolutionary dynamics to estimate the basic reproductive number (R0) and viral migration among host types in domestic and wild birds, as well as between the EA H5N8 and EA/NA H5N2 in wild birds. We did not find evidence to support hypothesis (i) or (ii) as our estimates of the transmission parameters suggested that the HPAIV outbreak met or exceeded the threshold for persistence in wild birds (R0 > 1) and poultry (R0 ≈ 1) with minimal estimated transmission among host types. There was also no evidence to support hypothesis (iii) because R0 values were similar among EA H5N8 and EA/NA H5N2 in wild birds. Our results suggest that this novel HPAIV and reassortments did not encounter any transmission barriers sufficient to prevent persistence when introduced to wild or domestic birds.