A preliminary description of the ecological characteristics of wild waterbird Japanese encephalitis virus hosts in high risk landscapes in India

Wild reservoirs of Japanese encephalitis virus are under-studied globally, which presents critical knowledge gaps for JEV infection ecology despite decades of received wisdom regarding this high-impact mosquito-borne virus. As a result, ardeid birds, generally understood to be the primary reservoirs for JEV, as well as other waterbirds occupying landscapes at high risk for spillover to humans, are frequently ignored by current surveillance mechanisms and infrastructure. This is particularly true in India, which experiences a high annual burden of human outbreaks. Incorporating wild reservoirs into surveillance of human and livestock populations is therefore essential but will first require a data-driven approach to target individual host species. The current study sought to define a preliminary ecological profile of JEV hosts based on 1) species ecological traits, and 2) species presence and abundance adjusted for the biotic constraints of sympatry. Optimal host species tended to be generalists and demonstrate regionally-increasing populations. While ardeid bird species richness, abundance, and relative abundance did demonstrate the strongest and most consistent associations with the distribution of human JEV outbreaks, this study also identified several individual species among two other bird families in these landscapes, the Anatidae and the Rallidae, which also exhibited an optimal host profile and were strongly associated with the distribution of outbreaks. The findings from this work provide the first data-driven evidence base to inform wildlife sampling for the monitoring of JEV circulation in outbreak hotspots in India and thus identify good preliminary targets for the development of One Health wildlife JEV surveillance.

Cryptosporidium and Giardia in Livestock in Tigray, Northern Ethiopia and Associated Risk Factors for Infection: A Cross-Sectional Study

The occurrence and species/genotypes of Cryptosporidium and Giardia duodenalis infecting young livestock in selected districts of Tigray, Ethiopia were investigated, along with risks associated with infection. A total of 757 faecal samples were collected from calves, lambs, and goat kids from four rural districts in Tigray, and also from calves in periurban Mekelle, Tigray's main city, and analysed for Cryptosporidium oocysts and Giardia cysts. Farmers answered questionnaires regarding potential risk factors at sample collection. Immunofluorescent antibody staining was used for parasite detection, and PCR at selected genes and sequencing of positive samples was used for molecular characterisation. The occurrence of Cryptosporidium infection was 10, 9, and 4% in calves, lambs, and goat kids, respectively; equivalent figures for Giardia infection were 39, 32, and 21%. Molecular characterisation of Cryptosporidium isolates revealed C. ubiquitum, subtype XIIa in all three host species; C. ryanae in calves and goat kids; C. andersoni and C. bovis were identified only in calves, and C. xiaoi was identified in lambs. For Giardia, Assemblage E predominated in all host species, but among calf isolates we also identified a few potentially zoonotic genotypes (assemblages A (AI) and Assemblage B). Periparturient care was shown to be a particularly relevant risk factor for infection, and infections were less likely to occur under extensive management systems. Our major findings were widespread occurrence of both parasites in livestock, and the apparent lack of the most common zoonotic species. Our results are discussed in relation to other relevant studies. As our study was conducted in Tigray, further investigation in different settings in Ethiopia could provide relevant information on transmission and zoonotic potential. In addition, given the dependency on healthy animals for the livelihoods of the population of Tigray, investigation of the effect of these common parasites on livestock productivity is important.

The Original Scientific Description of the Lone Star Tick (Amblyomma americanum, Acari: Ixodidae) and Implications for the Species’ Past and Future Geographic Distributions

Amblyomma americanum L. is an important vector in North America originally described by Linnaeus based on Pehr Kalm’s 1754 report. While Kalm’s ‘Travels into North America’ is well known, his 1754 report remains obscure. Some authors were skeptical that Kalm referred to A. americanum because he encountered them at sites farther north outside of the species’ range. However, the details in 1754 report leave no doubt that Kalm described lone star ticks. In this historical review, we provide support for Kalm’s identification using a modern translation of his 1754 report and other sources. We also delineate distributional changes of lone star ticks from the pre-colonization era to the present and interpret them in the context of large-scale anthropogenic changes in the landscape. In this framework, the lone star tick’s current northward expansion is a recolonization of their former range. Extensive deforestation and extirpation of their principal host species, white-tailed deer, led to A. americanum’s disappearance from the northern parts of its range by the 20th century. Subsequent recolonization by second-growth forest and increases in white-tailed deer populations by the mid-20th century is now allowing A. americanum to reclaim its former range. These changes in the land appear to be the driving force behind A. americanum’s present expansion. Understanding this species’ history and the factors contributing to its current expansion will enable better predictions about its future distribution and potential to transmit human pathogens.

A novel structure-based approach for identification of vertebrate susceptibility to SARS-CoV-2: implications for future surveillance programmes

Understanding the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a highly debatable and unsolved challenge for the scientific communities across the world. A key to dissect the susceptibility profiles of animal species to SARS-CoV-2 is to understand how virus enters into the cells. The interaction of SARS-CoV-2 ligands (RBD on spike protein) with its host cell receptor, angiotensin-converting enzyme 2 (ACE2), is a critical determinant of host range and cross-species transmission. In this study, we developed and implemented a rigorous computational approach for predicting binding affinity between 299 ACE2 orthologs from diverse vertebrate species and the SARS-CoV-2 spike protein. The findings show that the spike protein of SARS-CoV-2 can bind to many vertebrate species carrying evolutionary divergent ACE2, implying a broad host range at the virus entry level, which may contribute to cross-species transmission and further viral evolution. Additionally, the present study facilitated the identification of genetic determinants that may differentiate susceptible from the resistant host species based on the conservation of ACE2- spike protein interacting residues in vertebrate host species known to facilitate SARS-CoV-2 infection; however, these genetic determinants warrant in vivo experimental confirmation. The molecular interactions associated with varied binding affinity of distinct ACE2 isoforms in a specific bat species were identified using protein structure analysis, implying the existence of diversified susceptibility of bat species to SARS-CoV-2. The findings from current study highlight the importance of intensive surveillance programs aimed at identifying susceptible hosts, particularly those with the potential to transmit zoonotic pathogens, in order to prevent future outbreaks.

Dominance of coniferous and broadleaved trees drives bacterial associations with boreal feather mosses

The composition of ecologically important moss-associated bacterial communities seems to be mainly driven by host species, but may also be shaped by environmental conditions related with tree-canopy dominance. The moss phyllosphere has been studied in coniferous forests while broadleaf forests remain understudied. To determine if host species or environmental conditions defined by tree-canopy dominance drives the bacterial diversity in the moss phyllosphere, we used 16S rRNA gene amplicon sequencing to quantify changes in bacterial communities as a function of host species (Pleurozium schreberi and Ptilium crista-castrensis) and forest type (coniferous black spruce versus deciduous broadleaf trembling aspen) in eastern Canada. Forest type, not host species, was the main factor affecting moss phyllosphere bacterial community composition, though the interaction of both variables was significant. Bacterial α-diversity was highest in spruce forests, while there was greater turnover (β-diversity) and higher γ-diversity in aspen forests. Unexpectedly, Cyanobacteria were much more relatively abundant in aspen than in spruce forests, with the bacterial family Nostocaceae (Cyanobacteria) differing the most between both forest types. Our results suggest that the increasing change in dominance from coniferous to broadleaf trees due to natural and anthropic disturbances is likely to affect the composition of moss-associated bacteria in boreal forests.

Mammal virus diversity estimates are unstable due to accelerating discovery effort

Host-virus association data underpin research into the distribution and eco-evolutionary correlates of viral diversity and zoonotic risk across host species. However, current knowledge of the wildlife virome is inherently constrained by historical discovery effort, and there are concerns that the reliability of ecological inference from host-virus data may be undermined by taxonomic and geographical sampling biases. Here, we evaluate whether current estimates of host-level viral diversity in wild mammals are stable enough to be considered biologically meaningful, by analysing a comprehensive dataset of discovery dates of 6571 unique mammal host-virus associations between 1930 and 2018. We show that virus discovery rates in mammal hosts are either constant or accelerating, with little evidence of declines towards viral richness asymptotes, even in highly sampled hosts. Consequently, inference of relative viral richness across host species has been unstable over time, particularly in bats, where intensified surveillance since the early 2000s caused a rapid rearrangement of species' ranked viral richness. Our results illustrate that comparative inference of host-level virus diversity across mammals is highly sensitive to even short-term changes in sampling effort. We advise caution to avoid overinterpreting patterns in current data, since it is feasible that an analysis conducted today could draw quite different conclusions than one conducted only a decade ago.

Population genetic structure and phenotypic diversity of Aspidodera raillieti (Nematoda: Heterakoidea), a parasite of Didelphini marsupials in Brazil’s South and Southeast Atlantic Forest

Background: Population genetics of parasites may be influenced by host specificity, life-cycle, geographical distance, evolutionary history, and host-populations structure. The nematode Aspidodera raillieti infects different marsupial and rodent hosts in the Nearctic and Neotropical regions, implying a presumably significant gene flow among populations. However, niche diversification of A. raillieti main hosts in superimposed areas may provide conditions for population genetic structuring within this parasite species. We examined the genetic structuring of A. raillieti infecting three marsupial species co-occurring along South and Southeast Brazilian Atlantic Forest, a hotspot of biodiversity.Methods: We employed morphometric analyses and partial mitochondrial cytochrome c oxidase I gene sequences (MT-CO1) to characterize populations via phylogenetic and phylogeographic analyses.Results: Among 175 A. raillieti specimens recovered from marsupial hosts Didelphis aurita, D. albiventris, and Philander quica, we identified 99 MT-CO1 haplotypes forming four groups in phylogenetic trees and networks. Clades I and II encompassed parasites of D. albiventris from the South region, Clade III comprised parasites of D. aurita from the South and Southeast regions, and Clade IV encompassed parasites of D. aurita and D. albiventris from the South and Southeast regions and parasites of Philander quica from the South region. High genetic differentiation between clades, with a high fixation index and greater genetic variation in the analysis of molecular variance (AMOVA), indicated low gene flow between clades. Haplotypes shared among host species revealed a lack of host specificity. Significant correlation in the Mantel test, suggested parasite isolation by distance, although there was no evidence of geographic structure between populations. Negative values in neutrality tests for Clades III and IV suggested recent population expansion. Morphometric differentiation between A. raillieti specimens recovered from different host species, as well as from different localities, was more evident in males.Conclusion: The genetic structure of A. raillieti populations in the South and Southeast Atlantic Forest resulted from historical events rather than from current geographical distribution or host specificity. We also demonstrate morphometric variation associated with host species and localities, suggesting phenotypic plasticity to host attributes and to spatial variables.

Establishment and new hosts of the non-native seed beetle Stator limbatus (Coleoptera, Chrysomelidae, Bruchinae) on acacias in Europe

Stator limbatus is a phytophagous beetle native to warm regions of North and Central America, feeding on Fabaceae seeds and one of the most polyphagous species within the subfamily Bruchinae, here reported for the first time in Europe and on new hosts. Adult beetles emerged from Acacia spp. seeds collected in the islands of Corsica (France), and Sardinia (Italy). The wide presence in Sardinia and Corsica supports the hypothesis that this alien species was introduced several years ago. In both islands, S. limbatus emerged from Acacia mearnsii seeds, with infestation rates of up to 74.2 and 90.8% in 2019 and 2020, respectively. This seed beetle also emerged from two previously unreported host species, Acacia saligna and A. pycnantha, showing highest infestation rates of 4.0 and 95.1%, respectively. Both Acacia species are reported as new host associations with S. limbatus. Overall, seed infestation rates recorded in 2019 and 2020 indicate that S. limbatus is well established and that Mediterranean bioclimatic conditions are suitable for its population increase in size. This study lays the foundations for further research on known and potential host species and the spread and distribution of S. limbatus in Europe.

Development of an Online Tool for Pasteurella multocida Genotyping and Genotypes of Pasteurella multocida From Different Hosts

Pasteurella multocida is a versatile zoonotic pathogen. Multiple systems have been applied to type P. multocida from different diseases in different hosts. Recently, we found that assigning P. multocida strains by combining their capsular, lipopolysaccharide, and MLST genotypes (marked as capsular: lipopolysaccharide: MLST genotype) could help address the biological characteristics of P. multocida circulation in different hosts. However, there is still lack of a rapid and efficient tool to diagnose P. multocida according to this system. Here, we developed an intelligent genotyping platform PmGT for P. multocida strains according to their whole genome sequences using the web 2.0 technologies. By using PmGT, we determined capsular genotypes, LPS genotypes, and MLST genotypes as well as the main virulence factor genes (VFGs) of P. multocida isolates from different host species based on their whole genome sequences published on NCBI. The results revealed a closer association between the genotypes and pasteurellosis rather than between genotypes and host species. With the advent of high-quality, inexpensive DNA sequencing, PmGT represents a more efficient tool for P. multocida diagnosis in both epidemiological studies and clinical settings.