The genome sequence of the avian vampire fly (Philornis downsi), an invasive nest parasite of Darwin’s finches in Galápagos

The invasive avian vampire fly (Philornis downsi, Diptera: Muscidae) is considered one of the greatest threats to the endemic avifauna of the Galápagos Islands. The fly larvae parasitize nearly every passerine species, including Darwin’s finches. Most P. downsi research to date has focused on the effects of the fly on avian host fitness and mitigation methods. A lag in research related to the genetics of this invasion demonstrates, in part, the need to develop full-scale genomic resources with which to address further questions within this system. In this study, an adult female P. downsi was sequenced to generate a high-quality genome assembly. We examined various features of the genome (e.g., coding regions, non-coding transposable elements) and carried out comparative genomics analysis against other dipteran genomes. We identified lists of gene families that are significantly expanding or contracting in P. downsi that are related to insecticide resistance, detoxification, and counter defense against host immune responses. The P. downsi genome assembly provides an important resource for studying the molecular basis of successful invasion in the Galápagos and the dynamics of its population across multiple islands. The findings of significantly changing gene families associated with insecticide resistance and immune responses highlight the need for further investigations into the role of different gene families in aiding the fly’s successful invasion. Furthermore, this genomic resource provides a necessary tool to better inform future research studies and mitigation strategies aimed at minimizing the fly’s impact on Galápagos birds.

Description and Molecular Characterization of Two Species of Avian Blood Parasites, with Remarks on Circadian Rhythms of Avian Haematozoa Infections

Avian blood parasites are remarkably diverse and frequently occur in co-infections, which predominate in wildlife. This makes wildlife pathogen research challenging, particularly if they belong to closely related groups, resulting in diagnostic problems and poor knowledge about such infections as well as the patterns of their co-occurrence and interactions. This is particularly true due to the periodicity (circadian rhythms) of parasitemia, which means that different parasitemia and parasite stages might be found throughout the day. We analysed blood samples from a Eurasian blackbird (Turdus merula) and a Song thrush (Turdus philomelos). This study aimed to describe a new avian Lankesterella species and molecularly characterize and redescribe Splendidofilaria mavis, a common avian filarioid nematode. Additionally, it was possible to investigate the circadian rhythms of the avian blood parasites belonging to Plasmodium, Haemoproteus, Leucocytozoon, and Trypanosoma, which occurred in co-infection in the same avian host individuals. Different circadian rhythms were seen in different parasites, with Plasmodium sp. peaks occurring at midday, Leucocytozoon spp. peaks mainly during the evening and night, and Trypanosoma spp. and microfilariae peaks at midnight. No periodicity was seen in Haemoproteus and Lankesterella species infections. The time of parasitemia peaks most likely coincides with the time of vectors’ activity, and this should be beneficial for transmission. Knowledge about the circadian rhythms is needed for better understanding patterns in host-parasite interactions and disease transmission.

Prevalence and Histopathological Studies on Intestinal Cestode Parasite of Avian Host Gallus Domesticus (L) From Nashik Region, Maharashtra State, India

The lowest infection is recorded in rainy season and highest in summer season, may be due to life cycle stages and intermediate host availability increases in winter and became adult in definitive host in summer. No nematode and trematode parasite were considered and identified during the study period. Cysts were found deep in submucosa, although touches to serosa. The non-penetrative type of worms is Cotugnia sp. and Thaparea sp.; while the penetrative type of worm is Raillietina sp. and Paruterina sp. Free gravid segments mostly found in the posterior region of intestine while mature segments are freely suspended from scoleces in the lumen of intestine, only scoleces are attached, either superficially (non-penetrative type) or deep in submucosa (Penetrative type). Keywords: Cestode, histopathology, prevalence, hold-fast organs, Penetrative scolex

Identifying and prioritizing potential human-infecting viruses from their genome sequences

Determining which animal viruses may be capable of infecting humans is currently intractable at the time of their discovery, precluding prioritization of high-risk viruses for early investigation and outbreak preparedness. Given the increasing use of genomics in virus discovery and the otherwise sparse knowledge of the biology of newly discovered viruses, we developed machine learning models that identify candidate zoonoses solely using signatures of host range encoded in viral genomes. Within a dataset of 861 viral species with known zoonotic status, our approach outperformed models based on the phylogenetic relatedness of viruses to known human-infecting viruses (area under the receiver operating characteristic curve [AUC] = 0.773), distinguishing high-risk viruses within families that contain a minority of human-infecting species and identifying putatively undetected or so far unrealized zoonoses. Analyses of the underpinnings of model predictions suggested the existence of generalizable features of viral genomes that are independent of virus taxonomic relationships and that may preadapt viruses to infect humans. Our model reduced a second set of 645 animal-associated viruses that were excluded from training to 272 high and 41 very high-risk candidate zoonoses and showed significantly elevated predicted zoonotic risk in viruses from nonhuman primates, but not other mammalian or avian host groups. A second application showed that our models could have identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a relatively high-risk coronavirus strain and that this prediction required no prior knowledge of zoonotic Severe Acute Respiratory Syndrome (SARS)-related coronaviruses. Genome-based zoonotic risk assessment provides a rapid, low-cost approach to enable evidence-driven virus surveillance and increases the feasibility of downstream biological and ecological characterization of viruses.

Avian haemosporidians (Plasmodium and Haemoproteus) in selected bird groups (Old world Flycatchers, Warblers, Babblers, and Thrushes) of India and their phylogenetic relationships with other lineages of the world

We examined the Avian haemosporidians (Plasmodium and Haemoproteus) status in selected bird groups (Old world Flycatchers, Warblers, Babblers, and Thrushes) of India and their phylogenetic relationships with other known lineages of the world. The use of common genetic markers with information on the geographic distribution of parasite and host samples makes the data of avian haemosporidians genetic studies more comparable and infection source surveillance ready. The prevalence of Avian haemosporidians, in above bird groups from northern, eastern, and southern parts of India and the phylogenetic genetic analysis of genetic lineages was carried out at world level to know the possible source of infection. The MCC tree revealed six Haemosporidian lineages in which one was common (H_MSP01) and five were unique (H_CYOPOL01, H_CHD01, H_CYORUB01, H_EUMTHA01, and P_GEOCIT01). The avian host richness Index was 2.0852. 9.9%, prevalence of Haemosporidian infection was found in 111 DNA samples belonging to 6 host species. The Haemoproteus prevalence was found to be 9.0% across five host species (Phylloscopus trochiloides, Cyornis poliogenys, C. hainanus dialilaemus, C. rubeculoides, Eumiyas thalassinus) and Plasmodium prevalence was 0.9% in Geokichla citrina. The spatial phylogeny map showed possible source populations of hosts having H. pallidus lineages COLL2 and PFC1 infections in parts of Africa, Europe, North America, Malaysia, and Philippines. The Plasmodium lineage (P_GEOCIT01) showed a weak (93.89%) similarity with PADOM16 in Egypt. The statistical analysis suggested that the haemosporidian’s host species’ distribution range was directly and significantly associated with the altitude, minimum temperature, and relative humidity. H_MSP01 distribution was in accordance with H. pallidus having a wide geographic and host range.

First Report of Haemoproteus (Haemosporida, Haemoproteidae) Megalomeronts in the Brain of an Avian Host, with Description of Megalomerogony of Haemoproteus Pastoris, the Blood Parasite of the Common Starling

Species of Haemoproteus (Haemoproteidae, Haemosporida) are common bird pathogens. Recent molecular studies combined with histopathology research have reported development of megalomeronts of these parasites in various organs, sometimes resulting in the death of the avian host. Five Common starlings (Sturnus vulgaris) were found naturally infected with Haemoproteus pastoris lineage hLAMPUR01. The parasite was identified using microscopic examination of blood films and DNA sequences. Infected bird organs were investigated histologically for (i) the presence of exo-erythrocytic stages and (ii) the patterns of development (morphology and localization) in different host individuals. For the first time, megalomeronts of Haemoproteus parasites were seen developing in the brain, while numerous others at different stages of maturation were found in the intestine, pancreas, kidneys, lungs, esophagus, spleen, gizzard, and trachea. Megalomeronts were predominantly roundish or oval, up to 800 μm, they were surrounded by a capsular-like wall and developed asynchronously in the same bird individual. After megalomeront maturation and rupture, a massive infiltration of blood cells occurred, indicating the hemorrhagic processes. Review of available data showed that different Haemoproteus species produce markedly different megalomeronts, morphology of which can probably be predicted using phylogenetic analysis based on partial sequences of cytochrome b gene.

Integrating Spatiotemporal Epidemiology, Eco-Phylogenetics, and Distributional Ecology to Assess West Nile Disease Risk in Horses

Mosquito-borne West Nile virus (WNV) is the causative agent of West Nile disease in humans, horses, and some bird species. Since the initial introduction of WNV to the United States (US), approximately 30,000 horses have been impacted by West Nile neurologic disease and hundreds of additional horses are infected each year. Research describing the drivers of West Nile disease in horses is greatly needed to better anticipate the spatial and temporal extent of disease risk, improve disease surveillance, and alleviate future economic impacts to the equine industry and private horse owners. To help meet this need, we integrated techniques from spatiotemporal epidemiology, eco-phylogenetics, and distributional ecology to assess West Nile disease risk in horses throughout the contiguous US. Our integrated approach considered horse abundance and virus exposure, vector and host distributions, and a variety of extrinsic climatic, socio-economic, and environmental risk factors. Birds are WNV reservoir hosts, and therefore we quantified avian host community dynamics across the continental US to show intra-annual variability in host phylogenetic structure and demonstrate host phylodiversity as a mechanism for virus amplification in time and virus dilution in space. We identified drought as a potential amplifier of virus transmission and demonstrated the importance of accounting for spatial non-stationarity when quantifying interaction between disease risk and meteorological influences such as temperature and precipitation. Our results delineated the timing and location of several areas at high risk of West Nile disease and can be used to prioritize vaccination programs and optimize virus surveillance and monitoring.

Bactericidal activity of avian complement: a contribution to understand avian-host tropism of Lyme borreliae

Complement has been considered as an important factor impacting the host–pathogen association of spirochetes belonging to the Borrelia burgdorferi sensu lato complex, and may play a role in the spirochete’s ecology. Birds are known to be important hosts for ticks and in the maintenance of borreliae. Recent field surveys and laboratory transmission studies indicated that certain avian species act as reservoir hosts for different Borrelia species. Nevertheless, our current understanding of the molecular mechanisms determining host tropism of Borrelia is still in its fledgling stage. Concerning the role of complement in avian-host tropism, only a few bird species and Borrelia species have been analysed so far. Here, we performed in vitro serum bactericidal assays with serum samples collected from four bird species including the European robin Erithacus rubecula, the great tit Parus major, the Eurasian blackbird Turdus merula, and the racing pigeon Columba livia, as well as four Borrelia species (B. afzelii, B. garinii, B. valaisiana, and B. burgdorferi sensu stricto). From July to September 2019, juvenile wild birds were caught using mist nets in Portugal. Racing pigeons were sampled in a loft in October 2019. Independent of the bird species analysed, all Borrelia species displayed an intermediate serum-resistant or serum-resistant phenotype except for B. afzelii challenged with serum from blackbirds. This genospecies was efficiently killed by avian complement, suggesting that blackbirds served as dead-end hosts for B. afzelii. In summary, these findings suggest that complement contributes in the avian–spirochete–tick infection cycle and in Borrelia-host tropism.

Host and brood parasite coevolutionary interactions covary with comparative patterns of the avian visual system

In coevolutionary arms-races, reciprocal ecological interactions and their fitness impacts shape the course of phenotypic evolution. The classic example of avian host–brood parasite interactions selects for host recognition and rejection of increasingly mimetic foreign eggs. An essential component of perceptual mimicry is that parasitic eggs escape detection by host sensory systems, yet there is no direct evidence that the avian visual system covaries with parasitic egg recognition or mimicry. Here, we used eye size measurements collected from preserved museum specimens as a metric of the avian visual system for species involved in host–brood parasite interactions. We discovered that (i) hosts had smaller eyes compared with non-hosts, (ii) parasites had larger eyes compared with hosts before but not after phylogenetic corrections, perhaps owing to the limited number of independent evolutionary origins of obligate brood parasitism, (iii) egg rejection in hosts with non-mimetic parasitic eggs positively correlated with eye size, and (iv) eye size was positively associated with increased avian-perceived host–parasite eggshell similarity. These results imply that both host-use by parasites and anti-parasitic responses by hosts covary with a metric of the visual system across relevant bird species, providing comparative evidence for coevolutionary patterns of host and brood parasite sensory systems.

Vaccination against the Protozoan Parasite Histomonas meleagridis Primes the Activation of Toll-like Receptors in Turkeys and Chickens Determined by a Set of Newly Developed Multiplex RT-qPCRs

Histomonosis in turkeys and chickens is caused by the extracellular parasite Histomonas meleagridis, but the outcome of the disease varies depending on the host species. So far, studies on the immune response against histomonosis focus mainly on different traits of the adaptive immune system. Activation of toll like receptors (TLR) leads to the interplay between cells of innate and adaptive immunity with consequences on B and T cell clonal expansion. Therefore, the present investigation focused on the interaction of virulent and/or attenuated histomonads with the innate immune system of turkeys and chickens at 4, 10, 21 days post inoculation. The expression of TLRs (TLR1A, 1B, 2A, 2B, 3, 4, 5, 6(Tu), 7, 13(Tu) and 21(Ch)) and pro-inflammatory cytokines (IL1β and IL6) were analysed in caecum and spleen samples by RT-qPCR. Most frequent significant changes in expression levels of TLRs were observed in the caecum following infection with virulent parasites, an effect noticed to a lower degree in tissue samples from birds vaccinated with attenuated parasites. TLR1B, 2B and 4 showed a continuous up-regulation in the caecum of both species during infection or vaccination, followed by challenge with virulent parasites. Vaccinated birds of both species showed a significant earlier change in TLR expression following challenge than birds kept non-vaccinated but challenged. Expression of TLRs and pro-inflammatory cytokines were associated with severe inflammation of diseased birds in the local organ caecum. In the spleen, changes in TLRs and pro-inflammatory cytokines were less prominent and mainly observed in turkey samples. In conclusion, a detailed comparison of TLRs and pro-inflammatory cytokines of the innate immune system following inoculation with attenuated and/or virulent H. meleagridis of two avian host species provides an insight into regulative mechanisms of TLRs in the development of protection and limitation of the disease.