Epizootic Emergence Research Articles

Combined climate and regional mosquito habitat model based on machine learning

Besides invasive mosquito species also several native species are proven or suspected vectors of arboviruses as West Nile or Usutu virus in Western Europe. Habitat models of these native vectors can be a helpful tool for assessing the risk of autochthonous occurrence, outbreaks and spread of diseases caused by such arboviruses. Modelling native mosquitoes is complicated because of the perfect adaptation to the climatic and landscape conditions and their high abundance in contrast to invasive species. Here we present a new approach for such a habitat model for native mosquito species in Germany, which are considered as vectors of West Nile virus (WNV). Epizootic emergence of WNV was registered in Germany since 2018. The models are based on surveillance data of mosquitoes from the German citizen science project “Mückenatlas” complemented by data from systematic trap monitoring in Germany, and on data freely available from the Deutscher Wetterdienst (DWD) and OpenStreetMap (OSM). While climatic factors still play an important role, we could show that habitat suitability is predictable only by the combination of the climate model with a regional model. Both models were based on a machine-learning approach using XGBoost. Evaluation of the accuracy of the models was done by statistical analysis, determining among others feature importances using the SHAP-Library. Final output of the combined climatic and regional models are maps showing the superposed habitat suitability which are generated through a number of steps described in detail. These maps also include the registered cases of WNV infections in the selected region of Germany.

Novel murine models for studying Cache Valley virus pathogenesis and in utero transmission

ABSTRACT Cache Valley virus (CVV) is a prevalent emerging pathogen of significant importance to agricultural and human health in North America. Emergence in livestock can result in substantial agroeconomic losses resulting from the severe embryonic lethality associated with infection during pregnancy. Although CVV pathogenesis has been well described in ruminants, small animal models are still unavailable, which limits our ability to study its pathogenesis and perform preclinical testing of therapeutics. Herein, we explored CVV pathogenesis, tissue tropism, and disease outcomes in a variety of murine models, including immune -competent and -compromised animals. Our results show that development of CVV disease in mice is dependent on innate immune responses, and type I interferon signalling is essential for preventing infection in mice. IFN-αβR-/- mice infected with CVV present with significant disease and lethal infections, with minimal differences in age-dependent pathogenesis, suggesting this model is appropriate for pathogenesis-related, and short- and long-term therapeutic studies. We also developed a novel CVV in utero transmission model that showed high rates of transmission, spontaneous abortions, and congenital malformations during infection. CVV infection presents a wide tissue tropism, with significant amplification in liver, spleen, and placenta tissues. Immune-competent mice are generally resistant to infection, and only show disease in an age dependent manner. Given the high seropositivity rates in regions of North America, and the continuing geographic expansion of competent mosquito vectors, the risk of epidemic and epizootic emergence of CVV is high, and interventions are needed for this important pathogen.

West Nile Virus Epidemic in Germany Triggered by Epizootic Emergence, 2019.

One year after the first autochthonous transmission of West Nile virus (WNV) to birds and horses in Germany, an epizootic emergence of WNV was again observed in 2019. The number of infected birds and horses was considerably higher compared to 2018 (12 birds, two horses), resulting in the observation of the first WNV epidemy in Germany: 76 cases in birds, 36 in horses and five confirmed mosquito-borne, autochthonous human cases. We demonstrated that Germany experienced several WNV introduction events and that strains of a distinct group (Eastern German WNV clade), which was introduced to Germany as a single introduction event, dominated mosquito, birds, horse and human-related virus variants in 2018 and 2019. Virus strains in this clade are characterized by a specific-Lys2114Arg mutation, which might lead to an increase in viral fitness. Extraordinary high temperatures in 2018/2019 allowed a low extrinsic incubation period (EIP), which drove the epizootic emergence and, in the end, most likely triggered the 2019 epidemic. Spatiotemporal EIP values correlated with the geographical WNV incidence. This study highlights the risk of a further spread in Germany in the next years with additional human WNV infections. Thus, surveillance of birds is essential to provide an early epidemic warning and thus, initiate targeted control measures.

Burrow Dusting or Oral Vaccination Prevents Plague-Associated Prairie Dog Colony Collapse

Plague impacts prairie dogs (Cynomys spp.), the endangered black-footed ferret (Mustela nigripes) and other sensitive wildlife species. We compared efficacy of prophylactic treatments (burrow dusting with deltamethrin or oral vaccination with recombinant “sylvatic plague vaccine” [RCN-F1/V307]) to placebo treatment in black-tailed prairie dog (C. ludovicianus) colonies. Between 2013 and 2015, we measured prairie dog apparent survival, burrow activity and flea abundance on triplicate plots (“blocks”) receiving dust, vaccine or placebo treatment. Epizootic plague affected all three blocks but emerged asynchronously. Dust plots had fewer fleas per burrow (P < 0.0001), and prairie dogs captured on dust plots had fewer fleas (P < 0.0001) than those on vaccine or placebo plots. Burrow activity and prairie dog density declined sharply in placebo plots when epizootic plague emerged. Patterns in corresponding dust and vaccine plots were less consistent and appeared strongly influenced by timing of treatment applications relative to plague emergence. Deltamethrin or oral vaccination enhanced apparent survival within two blocks. Applying insecticide or vaccine prior to epizootic emergence blunted effects of plague on prairie dog survival and abundance, thereby preventing colony collapse. Successful plague mitigation will likely entail strategic combined uses of burrow dusting and oral vaccination within large colonies or colony complexes.

Correction: Epizootic Emergence of Usutu Virus in Wild and Captive Birds in Germany

The following information was missing from the Funding section: The study was also supported by the European Union FP7 project European Management Platform for Emerging and Reemerging Infectious Disease Entities (EMPERIE; no. 223498).

Epizootic emergence of Usutu virus in wild and captive birds in Germany

Background: Usutu virus (USUV) is an arthropod-borne, single-stranded RNA virus and belongs to the Japanese encephalitis virus group within the family Flaviviridae. USUV is closely related to West Nile virus, which killed thousands of birds in North America following its emergence in 1999. In 2001, USUV caused deaths in Blackbirds (Turdus merula) and Great Grey Owls (Strix nebulosa) in Austria. Two human cases with an USUV-related neuroinvasive illness were reported from Italy. In August 2010, USUV strain 1477 was isolated from a pool of Culex pipiens pipiens mosquitoes that were trapped in southwest Germany. In contrast, all mosquitoes trapped the year before in southwest Germany tested negative for USUV and no obvious increase in the mortality of birds was observed in southwest Germany in 2009 and 2010. Since June 2011, dead Blackbirds were frequently found in southwest Germany. Thus, our study aimed to identify the causative agent of this mass mortality in wild and captive birds in southwest Germany and to gather insights into the phylogenetic relationship and spatial distribution of the pathogen. Methods: Since June 2011, 223 dead birds were collected in southwest Germany and tested for the presence of viral pathogens with real-time RT-PCRs, immunohistochemistry and isolation methods. Results: USUV RNA was detected by real-time RT-PCR in 86 birds representing 6 species. The virus was isolated in cell culture from the heart of 14 Blackbirds. USUV-specific antigen was demonstrated by immunohistochemistry in brain, heart, liver, and lung of infected Blackbirds. The complete polyprotein coding sequence was obtained by deep sequencing of liver and spleen samples of a dead Blackbird. Phylogenetic analysis of the German USUV strain revealed a close relationship with strain Vienna that caused mass mortality among birds in Austria in 2001. Wild birds from lowland river valleys in southwest Germany were mainly affected by USUV, but also birds kept in aviaries. Conclusion: Our data suggest that after the initial detection of USUV in German mosquitoes in 2010, the virus spread in 2011 and caused epizootics among wild and captive birds in southwest Germany. The data also indicate an increased risk of USUV infections in humans in Germany.

Epizootic Emergence of Usutu Virus in Wild and Captive Birds in Germany

This study aimed to identify the causative agent of mass mortality in wild and captive birds in southwest Germany and to gather insights into the phylogenetic relationship and spatial distribution of the pathogen. Since June 2011, 223 dead birds were collected and tested for the presence of viral pathogens. Usutu virus (USUV) RNA was detected by real-time RT-PCR in 86 birds representing 6 species. The virus was isolated in cell culture from the heart of 18 Blackbirds (Turdus merula). USUV-specific antigen was demonstrated by immunohistochemistry in brain, heart, liver, and lung of infected Blackbirds. The complete polyprotein coding sequence was obtained by deep sequencing of liver and spleen samples of a dead Blackbird from Mannheim (BH65/11-02-03). Phylogenetic analysis of the German USUV strain BH65/11-02-03 revealed a close relationship with strain Vienna that caused mass mortality among birds in Austria in 2001. Wild birds from lowland river valleys in southwest Germany were mainly affected by USUV, but also birds kept in aviaries. Our data suggest that after the initial detection of USUV in German mosquitoes in 2010, the virus spread in 2011 and caused epizootics among wild and captive birds in southwest Germany. The data also indicate an increased risk of USUV infections in humans in Germany.

Retrospective space-time analysis of H5N1 Avian Influenza emergence in Thailand

BackgroundThe highly pathogenic avian influenza (HPAI) H5N1 virus remains a worldwide threat to human and animal health, while the mechanisms explaining its epizootic emergence and re-emergence in poultry are largely unknown. Data from Thailand, a country that experienced significant epidemics in poultry and has recorded suspicious cases of HPAI on a daily basis since 2004, are used here to study the process of emergence. A spatial approach is employed to describe all HPAI H5N1 virus epizootics from 2004 to 2008 and to characterize the pattern of emergence: multiple independent introductions of the virus followed by moderate local spread vs. very rare emergences followed by strong local spread and rare long range diffusion jumps. Sites where epizootics originate (by foreign introduction, local persistence, or long range jump) were selected from those to which the disease subsequently spreads using a filter based on relative date and position. The spatial distribution of these selected foci was statistically analyzed, and to differentiate environmental factors from long range diffusion, we investigate the relationship of these foci with environmental exposure factors and with rearing characteristics.ResultsDuring each wave of epizootics, the temporal occurrence of cases did not show a temporal interruption of more than a week. All foci were globally clustered; i.e., more than 90% of cases had a previous case within a 10 km range and a 21 day period of time, showing a strong local spread. We were able to estimate 60 km as the maximum distance for the local farm to farm dissemination process. The remaining "emergent" cases have occurred randomly over Thailand and did not show specific location, clusters, or trends. We found that these foci are not statistically related to specific environmental conditions or land cover characteristics, and most of them may be interpreted as long range diffusion jumps due to commercial practices.ConclusionWe conclude that only a few foci appear to have been at the origin of each HPAI epidemic wave, leading to the practical action that surveillance and control must focus on farm to farm transmission rather than on emergence or wild fauna.

Temporal dynamics of rabies in a wildlife host and the risk of cross-species transmission.

An epidemiological model was developed for rabies, linking the risk of disease in a secondary species (cats) to the temporal dynamics of disease in a wildlife reservoir (raccoons). Data were obtained from cats, raccoons, and skunks tested for rabies in the northeastern United States during 1992-2000. An epizootic algorithm defined a time-series of successive intervals of epizootic and inter-epizootic raccoon rabies. The odds of diagnosing a rabid cat during the first epizootic of raccoon rabies was 12 times greater than for the period prior to epizootic emergence. After the first raccoon epizootic, the risk for cat rabies remained elevated at levels six- to seven-fold above baseline. Increased monthly counts of rabid raccoons and skunks and decreasing human population density increased the probability of cat rabies in most models. Forecasting of the public health and veterinary burden of rabies and assessing the economics of control programmes, requires linking outcomes to dynamic, but predictable, changes in the temporal evolution of rabies epizootics.

Genetic diversity and relationships among Venezuelan equine encephalitis virus field isolates from Colombia and Venezuela.

During field studies of enzootic Venezuelan equine encephalitis (VEE) viruses associated with epizootic emergence, a large number of virus isolates were made in sylvatic foci of Venezuela and Colombia. To rapidly characterize these isolates, antigenic subtypes were determined by means of immunofluorescence and by single-strand conformational polymorphism (SSCP) analysis by use of an 856-bp fragment from the P62 gene, which we used to distinguish genetic variants. Representative isolates were sequenced to assess the sensitivity of SSCP to detect genetic differences. The SSCP analysis distinguished isolates differing by as little as 1 nucleotide; overall, differences of > or = 1 nucleotide were recognized 89% of the time, and the sensitivity to distinguish strains that differed by only 1 or 4 nucleotides was 17 and 57%, respectively. Phylogenetic analyses of representative sequences showed that all recent isolates from the Catatumbo region of western Venezuela and the middle Magdalena Valley of Colombia were closely related to epizootic subtype IAB and IC strains; strains from Yaracuy and Miranda States were more distantly related. Cocirculation of the same virus genotype in both Colombian and Venezuelan foci indicated that these viruses are readily transported between enzootic regions separated by > 300 km. The SSCP analysis appears to be a simple, fast, and relatively efficient method of screening VEE virus isolates to identify meaningful genetic variants.

Genetic and phenotypic changes accompanying the emergence of epizootic subtype IC Venezuelan equine encephalitis viruses from an enzootic subtype ID progenitor.

Recent studies have indicated that epizootic Venezuelan equine encephalitis (VEE) viruses can evolve from enzootic, subtype ID strains that circulate continuously in lowland tropical forests (A. M. Powers, M. S. Oberste, A. C. Brault, R. Rico-Hesse, S. M. Schmura, J. F. Smith, W. Kang, W. P. Sweeney, and S. C. Weaver, J. Virol. 71:6697-6705, 1997). To identify mutations associated with the phenotypic changes leading to epizootics, we sequenced the entire genomes of two subtype IC epizootic VEE virus strains isolated during a 1992-1993 Venezuelan outbreak and four sympatric, subtype ID enzootic strains closely related to the predicted epizootic progenitor. Analysis by maximum-parsimony phylogenetic methods revealed 25 nucleotide differences which were predicted to have accompanied the 1992 epizootic emergence; 7 of these encoded amino acid changes in the nsP1, nsP3, capsid, and E2 envelope glycoprotein, and 2 were mutations in the 3' untranslated genome region. Comparisons with the genomic sequences of IAB and other IC epizootic VEE virus strains revealed that only one of the seven amino acid changes associated with the 1992 emergence, a threonine-to-methionine change at position 360 of the nsP3 protein, accompanied another VEE virus emergence event. Two changes in the E2 envelope glycoprotein region believed to include the major antigenic determinants, both involving replacement of uncharged residues with arginine, are also candidates for epizootic determinants.

Genetic evidence for the origins of Venezuelan equine encephalitis virus subtype IAB outbreaks.

Epizootics of Venezuelan equine encephalitis (VEE) involving subtype IAB viruses occurred sporadically in South, Central and North America from 1938 to 1973. Incompletely inactivated vaccines have long been suspected as a source of the later epizootics. We tested this hypothesis by sequencing the PE2 glycoprotein precursor (1,677 nucleotides) or 26S/nonstructural protein 4 (nsP4) genome regions (4,490 nucleotides) for isolates representing most major outbreaks. Two distinct IAB genotypes were identified: 1) 1940s Peruvian strains and 2) 1938-1973 isolates from South, Central, and North America. Nucleotide sequences of these two genotypes differed by 1.1%, while the latter group showed only 0.6% sequence diversity. Early VEE virus IAB strains that were used for inactivated vaccine preparation had sequences identical to those predicted by phylogenetic analyses to be ancestors of the 1960s-1970s outbreaks. These data support the hypothesis of a vaccine origin for many VEE outbreaks. However, continuous, cryptic circulation of IAB viruses cannot be ruled out as a source of epizootic emergence.

Repeated emergence of epidemic/epizootic Venezuelan equine encephalitis from a single genotype of enzootic subtype ID virus.

Venezuelan equine encephalitis (VEE) epidemics and equine epizootics occurred periodically in the Americas from the 1920s until the early 1970s, when the causative viruses, subtypes IAB and IC, were postulated to have become extinct. Recent outbreaks in Columbia and Venezuela have renewed interest in the source of epidemic/epizootic viruses and their mechanism of interepizootic maintenance. We performed phylogenetic analyses of VEE virus isolates spanning the entire temporal and geographic range of strains available, using 857-nucleotide reverse transcription-PCR products including the E3 and E2 genes. Analyses indicated that epidemic/epizootic viruses are closely related to four distinct, enzootic subtype ID-like lineages. One of these lineages, which occurs in Columbia, Peru, and Venezuela, also included all of the epidemic/epizootic isolates; the remaining three ID-like lineages, which occur in Panama, Peru, Florida, coastal Ecuador, and southwestern Columbia, were apparently not associated with epizootic VEE emergence. Within the Columbia/Peru/Venezuela lineage, three distinct monophyletic groups of epidemic/epizootic viruses were delineated, indicating that VEE emergence has occurred independently at least three times (convergent evolution). Representative, complete E2 amino acid sequences were compared to identify potential determinants of equine virulence and epizootic emergence. Amino acids implicated previously in laboratory mouse attenuation generally did not vary among the natural isolates that we examined, indicating that they probably are not involved in equine virulence changes associated with VEE emergence. Most informative amino acids correlated with phylogenetic relationships rather than phenotypic characteristics, suggesting that VEE emergence has resulted from several distinct combinations of mutations that generate viruses with similar antigenic and equine virulence phenotypes.