Screening of wild deer populations for exposure to SARS-CoV-2 in the United Kingdom, 2020-2021.

Following findings in Northern America of SARS-CoV-2 infections in white-tailed deer, there is concern of similar infections in European deer and their potential as reservoirs of SARS-CoV-2 including opportunities for the emergence of new variants. UK deer sera were collected in 2020-2021 from 6 species and a hybrid with 1748 tested using anti-spike and anti-nucleocapsid serology assays. No samples were positive on both assays nor by surrogate neutralization testing. There is no evidence that spill-over infections of SARS-CoV-2 occurred from the human population to UK deer or that SARS-CoV-2 has been circulating in UK deer (over the study period). Although it cannot be ruled out, study results indicate that spill-over infections followed by circulation of SARS-CoV-2 to the most common European deer species is small.

Red and fallow deer determine the density of Ixodes ricinus nymphs containing Anaplasma phagocytophilum.

BACKGROUND: The density of Ixodes ricinus nymphs infected with Anaplasma phagocytophilum is one of the parameters that determines the risk for humans and domesticated animals to contract anaplasmosis. For this, I. ricinus larvae need to take a bloodmeal from free-ranging ungulates, which are competent hosts for A. phagocytophilum. METHODS: Here, we compared the contribution of four free-ranging ungulate species, red deer (Cervus elaphus), fallow deer (Dama dama), roe deer (Capreolus capreolus), and wild boar (Sus scrofa), to A. phagocytophilum infections in nymphs. We used a combination of camera and live trapping to quantify the relative availability of vertebrate hosts to questing ticks in 19 Dutch forest sites. Additionally, we collected questing I. ricinus nymphs and tested these for the presence of A. phagocytophilum. Furthermore, we explored two potential mechanisms that could explain differences between species: (i) differences in larval burden, which we based on data from published studies, and (ii) differences in associations with other, non-competent hosts. RESULTS: Principal component analysis indicated that the density of A. phagocytophilum-infected nymphs (DIN) was higher in forest sites with high availability of red and fallow deer, and to a lesser degree roe deer. Initial results suggest that these differences are not a result of differences in larval burden, but rather differences in associations with other species or other ecological factors. CONCLUSIONS: These results indicate that the risk for contracting anaplasmosis in The Netherlands is likely highest in the few areas where red and fallow deer are present. Future studies are needed to explore the mechanisms behind this association.

A combined transcriptomic approach to identify candidates for an anti-tick vaccine blocking B. afzelii transmission.

Ixodes ricinus is the vector for Borrelia afzelii, the predominant cause of Lyme borreliosis in Europe, whereas Ixodes scapularis is the vector for Borrelia burgdorferi in the USA. Transcription of several I. scapularis genes changes in the presence of B. burgdorferi and contributes to successful infection. To what extend B. afzelii influences gene expression in I. ricinus salivary glands is largely unknown. Therefore, we measured expression of uninfected vs. infected tick salivary gland genes during tick feeding using Massive Analysis of cDNA Ends (MACE) and RNAseq, quantifying 26.179 unique transcripts. While tick feeding was the main differentiator, B. afzelii infection significantly affected expression of hundreds of transcripts, including 465 transcripts after 24 h of tick feeding. Validation of the top-20 B. afzelii-upregulated transcripts at 24 h of tick feeding in ten biological genetic distinct replicates showed that expression varied extensively. Three transcripts could be validated, a basic tail protein, a lipocalin and an ixodegrin, and might be involved in B. afzelii transmission. However, vaccination with recombinant forms of these proteins only marginally altered B. afzelii infection in I. ricinus-challenged mice for one of the proteins. Collectively, our data show that identification of tick salivary genes upregulated in the presence of pathogens could serve to identify potential pathogen-blocking vaccine candidates.

Tripartite Interactions among Ixodiphagus hookeri, Ixodes ricinus and Deer: Differential Interference with Transmission Cycles of Tick-Borne Pathogens.

For the development of sustainable control of tick-borne diseases, insight is needed in biological factors that affect tick populations. Here, the ecological interactions among Ixodiphagus hookeri, Ixodes ricinus, and two vertebrate species groups were investigated in relation to their effects on tick-borne disease risk. In 1129 questing ticks, I. hookeri DNA was detected more often in I. ricinus nymphs (4.4%) than in larvae (0.5%) and not in adults. Therefore, we determined the infestation rate of I. hookeri in nymphs from 19 forest sites, where vertebrate, tick, and tick-borne pathogen communities had been previously quantified. We found higher than expected co-occurrence rates of I. hookeri with deer-associated Anaplasma phagocytophilum, and lower than expected rates with rodent-associated Borrelia afzelii and Neoehrlichia mikurensis. The prevalence of I. hookeri in nymphs varied between 0% and 16% and was positively correlated with the encounter probability of ungulates and the densities of all life stages of I. ricinus. Lastly, we investigated the emergence of I. hookeri from artificially fed, field-collected nymphs. Adult wasps emerged from seven of the 172 fed nymphs. From these observations, we inferred that I. hookeri is parasitizing I. ricinus larvae that are feeding on deer, rather than on rodents or in the vegetation. Since I. hookeri populations depend on deer abundance, the main propagation host of I. ricinus, these wasps have no apparent effect on tick populations. The presence of I. hookeri may directly interfere with the transmission cycle of A. phagocytophilum, but not with that of B. afzelii or N. mikurensis.

Presence of Roe Deer Affects the Occurrence of Anaplasma phagocytophilum Ecotypes in Questing Ixodes ricinus in Different Habitat Types of Central Europe.

The way in which European genetic variants of Anaplasma phagocytophilum circulate in their natural foci and which variants cause disease in humans or livestock remains thus far unclear. Red deer and roe deer are suggested to be reservoirs for some European A. phagocytophilum strains, and Ixodes ricinus is their principal vector. Based on groEL gene sequences, five A. phagocytophilum ecotypes have been identified. Ecotype I is associated with the broadest host range, including strains that cause disease in domestic animals and humans. Ecotype II is associated with roe deer and does not include zoonotic strains. In the present study, questing I. ricinus were collected in urban, pasture, and natural habitats in the Czech Republic, Germany, and Slovakia. A fragment of the msp2 gene of A. phagocytophilum was amplified by real-time PCR in DNA isolated from ticks. Positive samples were further analyzed by nested PCRs targeting fragments of the 16S rRNA and groEL genes, followed by sequencing. Samples were stratified according to the presence/absence of roe deer at the sampling sites. Geographic origin, habitat, and tick stage were also considered. The probability that A. phagocytophilum is a particular ecotype was estimated by a generalized linear model. Anaplasma phagocytophilum was identified by genetic typing in 274 I. ricinus ticks. The majority belonged to ecotype I (63.9%), 28.5% were ecotype II, and both ecotypes were identified in 7.7% of ticks. Ecotype II was more frequently identified in ticks originating from a site with presence of roe deer, whereas ecotype I was more frequent in adult ticks than in nymphs. Models taking into account the country-specific, site-specific, and habitat-specific aspects did not improve the goodness of the fit. Thus, roe deer presence in a certain site and the tick developmental stage are suggested to be the two factors consistently influencing the occurrence of a particular A. phagocytophilum ecotype in a positive I. ricinus tick.

Impact of vertebrate communities on Ixodes ricinus-borne disease risk in forest areas.

BACKGROUND: The density of questing ticks infected with tick-borne pathogens is an important parameter that determines tick-borne disease risk. An important factor determining this density is the availability of different wildlife species as hosts for ticks and their pathogens. Here, we investigated how wildlife communities contribute to tick-borne disease risk. The density of Ixodes ricinus nymphs infected with Borrelia burgdorferi (sensu lato), Borrelia miyamotoi, Neoehrlichia mikurensis and Anaplasma phagocytophilum among 19 forest sites were correlated to the encounter probability of different vertebrate hosts, determined by encounter rates as measured by (camera) trapping and mathematical modeling. RESULT: We found that the density of any tick life stage was proportional to the encounter probability of ungulates. Moreover, the density of nymphs decreased with the encounter probability of hare, rabbit and red fox. The density of nymphs infected with the transovarially-transmitted B. miyamotoi increased with the density of questing nymphs and the encounter probability of bank vole. The density of nymphs infected with all other pathogens increased with the encounter probability of competent hosts: bank vole for Borrelia afzelii and N. mikurensis, ungulates for A. phagocytophilum and blackbird for Borrelia garinii and Borrelia valaisiana. The negative relationship we found was a decrease in the density of nymphs infected with B. garinii and B. valaisiana with the encounter probability of wood mouse. CONCLUSIONS: Only a few animal species drive the densities of infected nymphs in forested areas. There, foxes and leporids have negative effects on tick abundance, and consequently on the density of infected nymphs. The abundance of competent hosts generally drives the abundances of their tick-borne pathogen. A dilution effect was only observed for bird-associated Lyme spirochetes.

Anaplasma phagocytophilum evolves in geographical and biotic niches of vertebrates and ticks.

BACKGROUND: Anaplasma phagocytophilum is currently regarded as a single species. However, molecular studies indicate that it can be subdivided into ecotypes, each with distinct but overlapping transmission cycle. Here, we evaluate the interactions between and within clusters of haplotypes of the bacterium isolated from vertebrates and ticks, using phylogenetic and network-based methods. METHODS: The presence of A. phagocytophilum DNA was determined in ticks and vertebrate tissue samples. A fragment of the groEl gene was amplified and sequenced from qPCR-positive lysates. Additional groEl sequences from ticks and vertebrate reservoirs were obtained from GenBank and through literature searches, resulting in a dataset consisting of 1623 A. phagocytophilum field isolates. Phylogenetic analyses were used to infer clusters of haplotypes and to assess phylogenetic clustering of A. phagocytophilum in vertebrates or ticks. Network-based methods were used to resolve host-vector interactions and their relative importance in the segregating communities of haplotypes. RESULTS: Phylogenetic analyses resulted in 199 haplotypes within eight network-derived clusters, which were allocated to four ecotypes. The interactions of haplotypes between ticks, vertebrates and geographical origin, were visualized and quantified from networks. A high number of haplotypes were recorded in the tick Ixodes ricinus. Communities of A. phagocytophilum recorded from Korea, Japan, Far Eastern Russia, as well as those associated with rodents had no links with the larger set of isolates associated with I. ricinus, suggesting different evolutionary pressures. Rodents appeared to have a range of haplotypes associated with either Ixodes trianguliceps or Ixodes persulcatus and Ixodes pavlovskyi. Haplotypes found in rodents in Russia had low similarities with those recorded in rodents in other regions and shaped separate communities. CONCLUSIONS: The groEl gene fragment of A. phagocytophilum provides information about spatial segregation and associations of haplotypes to particular vector-host interactions. Further research is needed to understand the circulation of this bacterium in the gap between Europe and Asia before the overview of the speciation features of this bacterium is complete. Environmental traits may also play a role in the evolution of A. phagocytophilum in ecotypes through yet unknown relationships.

The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts.

BACKGROUND: Small mammals are essential in the enzootic cycle of many tick-borne pathogens (TBP). To understand their contribution to the genetic diversity of Borrelia afzelii, the most prevalent TBP in questing Ixodes ricinus, we compared the genetic variants of B. afzelii at three distinct genetic loci. We chose two plasmid loci, dbpA and ospC, and a chromosomal one, IGS. RESULTS: While the larvae that fed on shrews (Sorex sp.) tested negative for B. afzelii, those fed on bank voles (Myodes glareolus) and wood mice (Apodemus sylvaticus) showed high infection prevalences of 0.13 and 0.27, respectively. Despite the high genetic diversity within B. afzelii, there was no difference between wood mice and bank voles in the number and types of B. afzelii haplotypes they transmit. CONCLUSIONS: The genetic diversity in B. afzelii cannot be explained by separate enzootic cycles in wood mice and bank voles.

Assessing the risk of human trichinellosis from pigs kept under controlled and non-controlled housing in Europe.

To support risk-based approach to prevent human trichinellosis, we estimated the human incidence for pigs originating from controlled and non-controlled housing, using a quantitative microbial risk assessment model for Trichinella (QMRA-T). Moreover, the effect of test sensitivity on human trichinellosis incidence from pigs from non-controlled housing was quantified. The estimated annual risk from pigs from non-controlled housing was 59,443 human trichinellosis cases without testing at meat inspection and 832 (95%CI 346-1410) cases with Trichinella testing, thus preventing 98.6% of trichinellosis cases per year by testing at meat inspection. Using the QMRA-T, a slight decrease in test sensitivity had a significant effect on the number of human trichinellosis cases from this housing type. The estimated annual risk for pigs from controlled housing was <0.002 (range 0.000-0.007) human cases with- and <0.010 (0.001-0.023) cases without Trichinella testing at meat inspection, which does not differ significantly (p = 0.2075). In practice, this means no cases per year irrespective of Trichinella testing. Thus controlled housing effectively prevents infection and Trichinella testing does not contribute to food safety for this housing type. Not testing for Trichinella requires evidence based full compliance with regulations for controlled housing.

Enzootic origins for clinical manifestations of Lyme borreliosis.

Both early localized and late disseminated forms of Lyme borreliosis are caused by Borrelia burgdorferi senso lato. Differentiating between the spirochetes that only cause localized skin infection from those that cause disseminated infection, and tracing the group of medically-important spirochetes to a specific vertebrate host species, are two critical issues in disease risk assessment and management. Borrelia burgdorferi senso lato isolates from Lyme borreliosis cases with distinct clinical manifestations (erythema migrans, neuroborreliosis, acrodermatitis chronica atrophicans, and Lyme arthritis) and isolates from Ixodes ricinus ticks feeding on rodents, birds and hedgehogs were typed to the genospecies level by sequencing part of the intergenic spacer region. In-depth molecular typing was performed by sequencing eight additional loci with different characteristics (plasmid-bound, regulatory, and housekeeping genes). The most abundant genospecies and genotypes in the clinical isolates were identified by using odds ratio as a measure of dominance. Borrelia afzelii was the most common genospecies in acrodermatitis patients and engorged ticks from rodents. Borrelia burgdorferi senso stricto was widespread in erythema migrans patients. Borrelia bavariensis was widespread in neuroborreliosis patients and in ticks from hedgehogs, but rare in erythema migrans patients. Borrelia garinii was the dominant genospecies in ticks feeding on birds. Spirochetes in ticks feeding on hedgehogs were overrepresented in genotypes of the plasmid gene ospC from spirochetes in erythema migrans patients. Spirochetes in ticks feeding on hedgehogs were overrepresented in genotypes of ospA from spirochetes in acrodermatitis patients. Spirochetes from ticks feeding on birds were overrepresented in genotypes of the plasmid and regulatory genes dbpA, rpoN and rpoS from spirochetes in neuroborreliosis patients. Overall, the analyses of our datasets support the existence of at least three transmission pathways from an enzootic cycle to a clinical manifestation of Lyme borreliosis. Based on the observations with these nine loci, it seems to be justified to consider the population structure of B. burgdorferi senso lato as being predominantly clonal.