Biology subjects

Pilgrim, J.

Publications and source records attributed to Pilgrim, J..

12 recordsLinked to original sources

bioRxiv2025

Mosquito Viromes in England and Wales Reveal Hidden Arbovirus Signals and Limited Ecological Structuring

Outbreaks of mosquito-borne viruses are increasing in temperate regions, with West Nile and Usutu viruses now established in wide regions across Europe, and both detected in the UK. Current surveillance strategies focus on targeted approaches which are well suited for monitoring established threats but limited in their ability to detect recently described or neglected viruses. High throughput sequencing (HTS) provides an unbiased alternative, allowing simultaneous identification of well-recognised and overlooked arboviruses, alongside insect-specific viruses (ISVs) that may modulate vector competence of the insects transmitting these pathogens. This study presents the first comprehensive virome survey of Culex mosquitoes in the UK, analysing populations collected from 93 sites across England and Wales through HTS and a systematic virus discovery pipeline. Across these sites, 41 distinct viral taxa were identified, including 11 novel species. Most viruses were rare or confined to a few sites, with only three detected in more than one third of sites, suggesting the absence of a broad conserved virome across populations. Within this diversity, three arbovirus-related lineages were detected: Hedwig virus (Peribunyaviridae), Umatilla virus (Sedoreoviridae), and Atherstone virus (Peribunyaviridae), the former two representing the first detections in the UK. These putative arboviruses were embedded in viral communities that showed minimal structuring by coarse land type but a modest decline in richness with latitude across rural sites, consistent with diversity gradients observed in other microbial systems. Together, these findings provide the first national-scale baseline of Culex mosquito-associated viral diversity in the UK, and demonstrate the value of metagenomic approaches in arbovirus preparedness.

microbiology↗

bioRxiv2025

Lack of Vector Competence in UK Culex pipiens molestus for Oropouche Virus

Oropouche virus (OROV) is an orthobunyavirus (Peribunyaviridae) that has caused recurrent outbreaks in South America and has recently expanded into the Caribbean, with various biting midge and mosquito species considered vectors. Recent imported cases to Europe and North America have raised concerns about the potential for local transmission in non-endemic areas. To assess this risk in the United Kingdom, we investigated the vector competence of Culex pipiens molestus (Cx. molestus), a human-biting mosquito common in urban environments. Laboratory-reared adult females were fed a bloodmeal containing a Cuban 2024 OROV outbreak strain (240023) and maintained at 27{degrees}C. Of 64 individuals tested at 12-s14 days post-infection via plaque assay, none were positive for OROV in bodies, indicating no evidence of infection and subsequently limited or no vector competence potential. These results provide evidence that UK populations of Cx. molestus are unlikely to support OROV transmission, thereby refining assessments of OROV emergence risk in temperate settings. Further studies are needed to test other putative UK mosquito vectors, as well as Culicoides biting midge species to fully assess the potential for OROV transmission in this region.

microbiology↗

bioRxiv2025

Emergence Risks from Within? Metagenomic Analysis of Mosquito Viromes from Two Zoos Reveals Mosquito-associated Orthobunyaviruses in the UK

In regions naive to mosquito-borne threats, risk assessments often prioritise incursion events, particularly those driven by climate change and host movement. However, these same factors may also facilitate the emergence of viruses already circulating in local vector populations. The use of metagenomics to assess mosquito viromes has expanded in recent decades, enabling the detection of both arboviruses and insect-specific viruses (ISVs), and helping to fill gaps in our understanding of virus circulation. In particular, zoological collections are potential interfaces for virus transmission between mosquitoes, animals, and humans, making them valuable sentinel sites for surveillance. Although mosquito virome studies have been conducted globally, UK mosquito populations remain comparatively understudied. To address this gap, we investigated the viromes of two key mosquito species, Culex pipiens s.l. and Culiseta annulata, through metagenomic sequencing of specimens collected at two UK zoos between 2021 and 2022. A total of 4,042 mosquitoes underwent sequencing across 44 pools, leading to the identification of 26 viral genomes, including nine novel species spanning RNA and DNA virus families. Viral distribution patterns revealed viruses shared across all pools, supporting the possibility of a conserved virome between mosquito species. Notably, two novel Orthobunyavirus species (Family Peribunyaviridae), Atherstone and Deva viruses, were detected. These represent the first documented mosquito-associated orthobunyaviruses in the UK, a genus that includes several known pathogens. Classification using the machine-learning tool MosViR suggests Atherstone virus, present at both zoos, is a putative arbovirus warranting further investigation. Supporting this is the presence of a non-structural protein S (NSs), a known virulence factor in orthobunyaviruses. In contrast, Deva virus had no NSs ORF and was not predicted to be an arbovirus. These findings improve our understanding of UK mosquito viruses, indicate possible risks to people or animals from orthobunyaviruses, and highlight the role of metagenomic surveillance in detecting emerging viral threats.

genomics↗

bioRxiv2025

Impact of temperature on vector competence of Culex pipiens molestus: implications for Usutu virus transmission in temperate regions

IntroductionUsutu virus (USUV) has been detected annually in the southeast of England since 2020. USUV RNA has been identified in wild birds and mosquito populations, and exposure of captive birds to USUV at Zoological Society of London (ZSL) has also been confirmed. Since its first detection in London, USUVs distribution has expanded across the South East, highlighting a need to understand the transmission dynamics of this virus in the UK. The primary vectors of USUV in the UK are likely Culex pipiens mosquitoes. Two biotypes have been identified, the bird-feeding Cx. pipiens pipiens and Cx. pipiens molestus which shows no restriction in host preference. The latter may play an important role in transmitting USUV from birds to humans. MethodsA laboratory colony of Cx. pipiens molestus mosquitoes were orally infected with the London strain of USUV and, incubated at 22 {degrees}C, 20 {degrees}C and 18{degrees} C for up to 28 days. Body samples and mosquito saliva samples were collected and analysed using a quantitative real-time reverse transcription PCR to determine infection and transmission potential, respectively. ResultsUSUV RNA was detected in all sample times at all temperatures assessed; with the highest temperature (22 {degrees}C) showing the greatest proportion of saliva and body positive samples. At this temperature, there was also an eight-fold increase in the relative viral copy number in the mosquito bodies, which was unobserved at other experimental temperatures. When a more sensitive PCR assay was used at the lowest experimental temperature used (18 {degrees}C) USUV RNA was present in the mosquito saliva and body samples for longer and showed a greater proportion of positive samples when compared to 20 {degrees}C. ConclusionThis study has demonstrated that Cx. pipiens molestus may be able to transmit USUV at 22 {degrees}C. Active replication of USUV was identified in the mosquito bodies at 22 {degrees}C but could not be demonstrated at lower temperatures, suggesting that 20 {degrees}C to 22 {degrees}C may be an important temperature threshold in USUV replication and transmission. Utilisation of a more sensitive assay for the lower experimental temperatures revealed that USUV was detectable at 18 {degrees}C. Therefore, when conducting infection studies on temperate mosquito-borne viruses, it is important to consider assay sensitivity.

molecular biology↗

bioRxiv2024

Meta-analyses of Culex blood-meals indicates strong regional effect on feeding patterns

Understanding host utilization by mosquito vectors is essential to assess the risk of vector-borne diseases. Many studies have investigated the feeding patterns of Culex mosquitoes by molecular analysis of blood-meals from field collected mosquitoes. However, these individual small-scale studies only provide a limited understanding of the complex host-vector interactions when considered in isolation. Here, we analyse the Culex blood-feeding data from 90 publications over the last 15 years to give a global insight into the feeding patterns of Culex mosquitoes, with particular reference to vectors of currently emerging Culex-borne viruses such as West Nile and Usutu. Data on 26,857 blood-meals from 71 different Culex species were extracted from published literature. The percentage of blood-meals on amphibian, avian, human, non-human mammalian, and reptilian hosts was determined for each Culex species. Our analysis showed that feeding patterns were not significantly explained by mosquito species-level phylogeny, indicating that external factors play an important role in determining mosquito feeding patterns. For Cx. quinquefasciatus, Cx. pipiens complex, and Cx. tritaeniorhynchus, feeding patterns were compared across the worlds seven biogeographical realms. Culex tritaeniorhynchus, Cx. pipiens complex and Cx. quinquefasciatus all had significantly varied feeding patterns between realms. These results demonstrate that feeding patterns of Culex mosquitoes vary between species but can also vary between geographically distinct populations of the same species, indicating that regional or population-level adaptations are major drivers of host utilization. Ultimately, these findings support the surveillance of vector-borne diseases by specifying which host groups are most likely to be at risk. Author summaryBeing aware of mosquito biting behaviour is essential to determine the threat of mosquito-borne diseases. Studying the feeding patterns of Culex mosquitoes is crucial as these mosquitoes are vectors of currently emerging or re-emerging arboviruses such as West Nile and Usutu. Feeding behaviour of Culex mosquitoes has been examined in many individual small-scale studies. These studies only focus on the feeding patterns in a specific area. To gain a more global understanding of these feeding patterns we analysed all available Culex blood-feeding data from the last 15 years. In summary, data on 26,857 blood-meals from 71 different Culex species was collected. For each species the percentage of blood-meals on different host groups was determined. We analysed the relationship between feeding patterns and mosquito phylogeny, which showed that phylogeny alone could not explain feeding patterns. These results indicate that external factors such as land use and climate could play an important role in determining feeding patterns. For further analysis we determined the feeding patterns for three important vector species, Cx. quinquefasciatus, Cx. pipiens complex, and Cx. tritaeniorhynchus in different biogeographical realms. All three species showed different feeding patterns in the included realms. Thus, the same species can have different feeding patterns in different regions, indicating the importance of local surveillance.

ecology↗

bioRxiv2023

Features that matter: evolutionary signatures that predict viral transmission routes

Routes of virus transmission between hosts are key to understanding viral epidemiology. Different routes have large effects on viral ecology, and likelihood and rate of transmission. For example, respiratory and vector-borne viruses together encompass the majority of high-consequence animal and plant outbreaks. However, the specific transmission route(s) can take months to years to determine, undermining the efficiency of mitigation efforts. Here, we identify the vial features and evolutionary signatures which are predictive of viral transmission routes, and use them to predict potential routes for fully-sequenced viruses - we perform this for both viruses with no observed routes, as well as viruses with missing routes. This was achieved by compiling a dataset of 24,953 virus-host associations with 81 defined transmission routes, constructing a hierarchy of virus transmission encompassing those routes and 42 higher-order modes, and engineering 446 predictive features from three complementary perspectives. We integrated those data and features, to train 98 independent ensembles of LightGBM classifiers, each incorporating five different class-balancing approaches. Using our trained ensembles, we demonstrated that all features contributed to the prediction for at least one of routes and/or modes of transmission, demonstrating the utility of our multi-perspective approach. Our approach achieved ROC-AUC=0.991, and F1-score=0.855 across all modelled transmission mechanisms; and was able to achieve high levels of predictive performance for high-consequence respiratory (ROC-AUC=0.990, and F1-score=0.864) and vector-borne transmission (ROC-AUC=0.997, and F1-score=0.921). Our framework ranks the viral features in order of their contribution to prediction, per transmission route, and hence identifies the genomic evolutionary signatures associated with each route. Together with the more matured field of viral host-range prediction, our predictive framework could: provide early insights into the potential for, and pattern of viral spread; facilitate rapid response with appropriate measures; and significantly triage the time-consuming investigations to confirm the likely routes of transmission. Moreover, the performance of our approach in high-consequence transmission routes showcases that our methodology has direct utility to pandemic preparedness. AUTHORS SUMMARYRoutes of virus transmission - the mechanism(s) by which a virus physically gets from an infected to an uninfected host, are crucial to understanding how viral diseases spread among animals and plants. Here, we uncover the evolutionary signatures which can predict the transmission routes a virus uses to move from one host to another, enabling us to identify any unobserved routes for known viruses and even predict potential routes of newly emerged viruses. We first compile a comprehensive dataset of virus-host associations. Leveraging this dataset, we employ a multi-perspective machine learning approach to achieve high predictive performance. Our framework ranks viral features by their significance in prediction, revealing genomic evolutionary signatures linked to each route. Our approach could provide early insights into viral spread patterns, facilitating prompt response efforts to new outbreaks and epidemics, and streamline laboratory investigations. Overall, our study represents a step forward in our ability to anticipate and mitigate the impact of emerging infectious diseases on human, animal, and plant health.

ecology↗

bioRxiv2022

Emerging variants of canine enteric coronavirus associated with seasonal outbreaks of severe canine gastroenteric disease

Canine enteric coronavirus (CECoV) variants have an emerging role in severe outbreaks of canine gastroenteritis. Here we used syndromic health data from a sentinel network of UK veterinary practices to identify an outbreak of severe canine gastroenteritis. Affected dogs frequently presented with vomiting, diarrhoea and inappetence. Data from sentinel diagnostic laboratories showed similar seasonal increases in CECoV diagnosis. Membrane glycoprotein (M) gene sequence analysis implied wide geographical circulation of a new CECoV variant. Whole genome sequencing suggested the main circulating 2022 variant was most closely related to one previously identified in 2020 with additional spike gene recombination; all variants were unrelated to CECoV-like viruses recently associated with human respiratory disease. Identifying factors that drive population-level evolution, and its implications for host protection and virulence, will be important to understand the emerging role of CECoV variants in canine and human health, and may act as a model for coronavirus population adaptation more widely.

genomics↗

bioRxiv2022

Monkeypox virus shows potential to infect a diverse range of native animal species across Europe, indicating high risk of becoming endemic in the region

BackgroundMonkeypox is a zoonotic virus which persists in animal reservoirs and periodically spills over into humans, causing outbreaks. During the current 2022 outbreak, monkeypox virus has persisted via human-human transmission, across all major continents and for longer than any previous record. This unprecedented spread creates the potential for the virus to spillback into local susceptible animal populations. Persistent transmission amongst such animals raises the prospect of monkeypox virus becoming enzootic in new regions. However, the full and specific range of potential animal hosts and reservoirs of monkeypox remains unknown, especially in newly at-risk non-endemic areas. MethodsHere, utilising ensembles of classifiers comprising different class balancing techniques and incorporating instance weights, we identify which animal species are potentially susceptible to monkeypox virus. Subsequently, we generate spatial distribution maps to highlight high-risk geographic areas at high resolution. FindingsWe show that the number of potentially susceptible species is currently underestimated by 2.4 to 4.3-fold, and that a high density of wild susceptible species are native to Europe. We provide lists of these species, and highlight high-risk hosts for spillback and potential long-term reservoirs, which may enable monkeypox virus to become endemic. InterpretationWe highlight the European red fox and brown rat, as they have established interactions with potentially contaminated urban waste and sewage, which provides a mechanism for potential spillback. We anticipate that our results will enable targeted active surveillance of potential spillback event, to minimise risk of the virus becoming endemic in these regions. Our results also indicate the potential of domesticated cats and dogs (latter now confirmed) being susceptible to monkeypox virus, and hence support many health organisations advice for infected humans to avoid physical interaction with pets.

ecology↗

bioRxiv2021

Large-scale comparative genomics unravels great genomic diversity across the Rickettsia and Ca. Megaira genera and identifies Torix group as an evolutionarily distinct clade.

Rickettsia are intracellular bacteria originally described as arthropod borne pathogens that are emerging as a diverse group of often biologically important, non-pathogenic symbionts of invertebrates and microeukaryotes. However, sparse genomic resources for symbiotic strains and for the sister genus (Candidatus Megaira) inhibit our understanding of Rickettsia evolution and biology. Here, we present the first closed genomes of Ca. Megaira from an alga (Mesostigma viride), and Torix Rickettsia from midge (Culicoides impunctatus) and bed bug (Cimex lectularius) hosts. Additionally, we sequenced and constructed draft genomes for Ca. Megaira from another alga (Carteria cerasiformis), Transitional group Rickettsia from tsetse fly (Glossina morsitans submorsitans), and Torix Rickettsia from a spider mite (Bryobia graminum). We further extract 22 draft genomes from arthropod genome sequencing projects, including 1 Adalia, 4 Transitional, 1 Spotted Fever, 7 Torix, 7 Belli and the first Rhyzobius and Meloidae Rickettsia group genomes. We used new and existing Rickettsia genomes to estimate the phylogeny and metabolic potential across groups and reveal transitions in genomic properties. These data reveal Torix as unique amongst currently described Rickettsia, with highly distinct and diverse accessory genomes. We confirm the presence of a third subclade of Torix, previously only known from gene marker sequences. Further, Torix share an intact pentose phosphate pathway with Ca. Megaira, not observed in other Rickettsia. Considering the distinctness and diversity of Torix, we propose that the group be named Candidatus Tisiphia. The wide host range of Ca. Tisiphia symbionts necessitates onward research to understand the biological and physiological bases of Ca. Tisiphia-host interactions. Importance statementMembers of the genus Rickettsia were originally identified as causative agents of mammalian vector-borne disease. In the last 25 years we have recognised that many Rickettsia are arthropod symbionts, and sit alongside a sister taxon, Ca. Megaira, which are symbiotic associates of microeukaryotes. The lack of genomic information for symbiotic strains affects our ability to determine the evolutionary relationships between strains and understand the biological underpinnings of the different symbioses. We clarify these relationships by assembling 26 genomes of Rickettsia from understudied groups, and the first two Ca. Megaira, from various insects and microeukaryotes. Of note, the accessory genome diversity and broad host range of Torix Rickettsia parallels all other Rickettsia combined. This diversity, alongside the breadth of host species, make the Torix clade an important hidden player in invertebrate biology and physiology. We argue this clade should be given its own genus status, for which we propose Ca. Tisiphia.

microbiology↗

bioRxiv2020

Identifying candidate Culicoides spp. (Diptera: Ceratopogonidae) for the study of interactions with Candidatus Cardinium hertigii (Bacteroidetes).

Culicoides biting midges (Diptera: Ceratopogonidae) are disease vectors responsible for the transmission of several viruses of economic and animal health importance. The recent deployment of Wolbachia with pathogen-blocking capacity to control viral disease transmission by mosquitoes has led to a focus on the potential use of endosymbionts to control arboviruses transmitted by other vector species. Previous screens of Culicoides have described the presence of Candidatus Cardinium hertigii (Bacteroidetes). However, the biological impact of this symbiont is yet to be uncovered and awaits a suitable system to study Cardinium-midge interactions. To identify candidate species to investigate these interactions, accurate knowledge of the distribution of the symbiont within Culicoides populations is needed. We used a sensitive nested PCR assay to screen Cardinium infection in 337 individuals of 25 Culicoides species from both Palearctic and Afrotropical regions. Infections were observed in several vector species including C. imicola and the pulicaris complex (C. pulicaris, C. bysta, C. newsteadi and C. punctatus) with prevalence ranging from low and intermediate, to fixation. Infection in C. pulicaris was very rare in comparison to a previous study, and there is evidence the prior record of high prevalence represents a laboratory contamination error. Phylogenetic analysis based on the Gyrase B gene sequence grouped all new isolates within "group C" of the genus, a clade which has to date been exclusively described in Culicoides. Through a comparison of our results with previous screens, we evaluate the suitability of Cardinium-infected species for future work pertaining to the symbiont.

microbiology↗

bioRxiv2020

Cardinium symbiosis as a potential confounder of mtDNA based phylogeographic inference in Culicoides imicola (Diptera: Ceratopogonidae), a vector of veterinary viruses

Culicoides imicola (Diptera: Ceratopogonidae) is an important Afrotropical and Palearctic vector of disease, transmitting viruses of animal health and economic significance. The apparent incursions of C. imicola into mainland Europe via wind-movement events has made it important to trace this species to better predict new areas of arbovirus outbreaks. A widely used method for tracking dispersal patterns of C. imicola employs a phylogeographic approach anchored on the mtDNA marker COI (cytochrome c oxidase subunit I). However, a problem with this approach is that maternally-inherited symbiotic bacteria can alter the frequency of COI mitochondrial haplotypes (mitotypes), masking the true patterns of movement and gene flow. In this study, we investigate possible associations of the symbiont Cardinium with C. imicola mitotype distribution. Haplotype network analysis indicates the concordance of specific mitotypes with Cardinium infection status in C. imicola populations from the Mediterranean basin and South Africa. This observation urges caution on the single usage of the COI marker to determine population structure and movement in C. imicola, and instead suggests the complementary utilisation of additional molecular markers (e.g. microsatellites and nuclear markers).

microbiology↗

bioRxiv2020

The Tissue Tropisms and Transstadial Transmission of a Rickettsia Endosymbiont in the Highland Midge, Culicoides impunctatus (Diptera: Ceratopogonidae)

Rickettsia are a group of intracellular bacteria which can manipulate host reproduction and alter sensitivity to natural enemy attack in a diverse range of arthropods. The maintenance of Rickettsia endosymbionts in insect populations can be achieved through both vertical and horizontal transmission routes. For example, the presence of the symbiont in the follicle cells and salivary glands of Bemisia whiteflies allows Belli group Rickettsia transmission via the germline and plants, respectively. However, the transmission routes of other Rickettsia, such as those in the Torix group of the genus, remain underexplored. Through fluorescence in-situ hybridisation (FISH) and transmission electron microscopy (TEM) screening, this study describes the pattern of Torix Rickettsia tissue tropisms in the highland midge, Culicoides impunctatus (Diptera: Ceratopogonidae). Of note is high intensity of infection of the ovarian suspensory ligament, suggestive of a novel germline targeting strategy. Additionally, localisation of the symbiont in tissues of several developmental stages suggests transstadial transmission is a major route of ensuring maintenance of Rickettsia within C. impunctatus populations. Aside from providing insights into transmission strategies, Rickettsia presence in the fat body of larvae indicates potential host fitness and vector capacity impacts to be investigated in the future. Importance StatementMicrobial symbionts of disease vectors have garnered recent attention due to their ability to alter vectorial capacity. Their consideration as a means of arbovirus control depends on symbiont vertical transmission which leads to spread of the bacteria through a population. Previous work has identified a Rickettsia symbiont present in several vector species of biting midges (Culicoides spp.), however, symbiont transmission strategies and host effects remain underexplored. In this study, we describe the presence of Rickettsia in the ovarian suspensory ligament and the ovarian epithelial sheath of Culicoides impunctatus. Infection of these organs suggest the connective tissue surrounding developing eggs is important for ensuring vertical transmission of the symbiont in midges and possibly other insects. Additionally, our results indicate Rickettsia localisation in the fat body of Culicoides impunctatus. As viruses spread by midges often replicate in the fat body, this implies possible vector competence effects to be further investigated.

microbiology↗