Synchronicity of viral shedding in molossid bat maternity colonies.

Infection dynamics in vertebrates are driven by biological and ecological processes. For bats, population structure and reproductive cycles have major effects on RNA virus transmission. On Reunion Island, previous studies have shown that parturition of pregnant females and aggregation of juvenile Reunion free-tailed bats (Mormopterus francoismoutoui) are associated with major increase in the prevalence of bats shedding RNA viruses. The synchronicity of such shedding pulses, however, is yet to be assessed between viruses but also maternity colonies. Based on 3422 fresh faeces collected every 2-5 weeks during four consecutive birthing seasons, we report the prevalence of bats shedding astroviruses (AstVs), coronaviruses (CoVs) and paramyxoviruses (PMVs) in two maternity colonies on Reunion Island. We found that the proportion of bats shedding viruses is highly influenced by sampling collection periods, and therefore by the evolution of the population age structure. We highlight that virus shedding patterns are consistent among years and colonies for CoVs and to a lesser extent for PMVs, but not for AstVs. We also report that 1% of bats harbour co-infections, with two but not three of the viruses, and most co-infections were due to CoVs and PMVs.

Influenza A virus on oceanic islands: host and viral diversity in seabirds in the Western Indian Ocean.

Ducks and seabirds are natural hosts for influenza A viruses (IAV). On oceanic islands, the ecology of IAV could be affected by the relative diversity, abundance and density of seabirds and ducks. Seabirds are the most abundant and widespread avifauna in the Western Indian Ocean and, in this region, oceanic islands represent major breeding sites for a large diversity of potential IAV host species. Based on serological assays, we assessed the host range of IAV and the virus subtype diversity in terns of the islands of the Western Indian Ocean. We further investigated the spatial variation in virus transmission patterns between islands and identified the origin of circulating viruses using a molecular approach. Our findings indicate that terns represent a major host for IAV on oceanic islands, not only for seabird-related virus subtypes such as H16, but also for those commonly isolated in wild and domestic ducks (H3, H6, H9, H12 subtypes). We also identified strong species-associated variation in virus exposure that may be associated to differences in the ecology and behaviour of terns. We discuss the role of tern migrations in the spread of viruses to and between oceanic islands, in particular for the H2 and H9 IAV subtypes.

The Recent Evolution of a Maternally-Inherited Endosymbiont of Ticks Led to the Emergence of the Q Fever Pathogen, Coxiella burnetii.

Q fever is a highly infectious disease with a worldwide distribution. Its causative agent, the intracellular bacterium Coxiella burnetii, infects a variety of vertebrate species, including humans. Its evolutionary origin remains almost entirely unknown and uncertainty persists regarding the identity and lifestyle of its ancestors. A few tick species were recently found to harbor maternally-inherited Coxiella-like organisms engaged in symbiotic interactions, but their relationships to the Q fever pathogen remain unclear. Here, we extensively sampled ticks, identifying new and atypical Coxiella strains from 40 of 58 examined species, and used this data to infer the evolutionary processes leading to the emergence of C. burnetii. Phylogenetic analyses of multi-locus typing and whole-genome sequencing data revealed that Coxiella-like organisms represent an ancient and monophyletic group allied to ticks. Remarkably, all known C. burnetii strains originate within this group and are the descendants of a Coxiella-like progenitor hosted by ticks. Using both colony-reared and field-collected gravid females, we further establish the presence of highly efficient maternal transmission of these Coxiella-like organisms in four examined tick species, a pattern coherent with an endosymbiotic lifestyle. Our laboratory culture assays also showed that these Coxiella-like organisms were not amenable to culture in the vertebrate cell environment, suggesting different metabolic requirements compared to C. burnetii. Altogether, this corpus of data demonstrates that C. burnetii recently evolved from an inherited symbiont of ticks which succeeded in infecting vertebrate cells, likely by the acquisition of novel virulence factors.

The role of seabirds of the Iles Eparses as reservoirs and disseminators of parasites and pathogens.

The role of birds as reservoirs and disseminators of parasites and pathogens has received much attention over the past several years due to their high vagility. Seabirds are particularly interesting hosts in this respect. In addition to incredible long-distance movements during migration, foraging and prospecting, these birds are long-lived, site faithful and breed in dense aggregations in specific colony locations. These different characteristics can favor both the local maintenance and large-scale dissemination of parasites and pathogens. The Iles Eparses provide breeding and feeding grounds for more than 3 million breeding pairs of seabirds including at least 13 species. Breeding colonies on these islands are relatively undisturbed by human activities and represent natural metapopulations in which seabird population dynamics, movement and dispersal can be studied in relation to that of circulating parasites and pathogens. In this review, we summarize previous knowledge and recently-acquired data on the parasites and pathogens found in association with seabirds of the Iles Eparses. These studies have revealed the presence of a rich diversity of infectious agents (viruses, bacteria and parasites) carried by the birds and/or their local ectoparasites (ticks and louse flies). Many of these agents are widespread and found in other ecosystems confirming a role for seabirds in their large scale dissemination and maintenance. The heterogeneous distribution of parasites and infectious agents among islands and seabird species suggests that relatively independent metacommunities of interacting species may exist within the western Indian Ocean. In this context, we discuss how the patterns and determinants of seabird movements may alter parasite and pathogen circulation. We conclude by outlining key aspects for future research given the baseline data now available and current concerns in eco-epidemiology and biodiversity conservation.

Leptospira and paramyxovirus infection dynamics in a bat maternity enlightens pathogen maintenance in wildlife.

Bats are reservoirs for several zoonotic pathogens of medical importance; however, infection dynamics of pathogens in wild bat populations remain poorly understood. Here, we examine the influence of host crowding and population age structure on pathogen transmission and diversity in bat populations. Focusing on two pathogen taxa of medical importance, Leptospira bacteria and paramyxoviruses, we monitored host population and pathogen shedding dynamics within a maternity colony of the tropical bat species Mormopterus francoismoutoui, endemic to Réunion Island. Our data reveal astonishingly similar infection dynamics for Leptospira and paramyxoviruses, with infection peaks during late pregnancy and 2 months after the initial birth pulse. Furthermore, although co-infection occurs frequently during the peaks of transmission, the patterns do not suggest any interaction between the two pathogens. Partial sequencing reveals a unique bat-specific Leptospira strain contrasting with the co-circulation of four separate paramyxovirus lineages along the whole breeding period. Patterns of infection highlight the importance of host crowding in pathogen transmission and suggest that most bats developed immune response and stop excreting pathogens. Our results support that bat maternity colonies may represent hot spots of transmission for bacterial and viral infectious agents, and highlight how seasonality can be an important determinant of host-parasite interactions and disease emergence.

Highly diverse morbillivirus-related paramyxoviruses in wild fauna of the southwestern Indian Ocean Islands: evidence of exchange between introduced and endemic small mammals.

UNLABELLED: The Paramyxoviridae form an increasingly diverse viral family, infecting a wide variety of different hosts. In recent years, they have been linked to disease emergence in many different animal populations and in humans. Bats and rodents have been identified as major animal populations capable of harboring paramyxoviruses, and host shifting between these animals is likely to be an important driving factor in the underlying evolutionary processes that eventually lead to disease emergence. Here, we have studied paramyxovirus circulation within populations of endemic and introduced wild small mammals of the southwestern Indian Ocean region and belonging to four taxonomic orders: Rodentia, Afrosoricida, Soricomorpha, and Chiroptera. We report elevated infection levels as well as widespread paramyxovirus dispersal and frequent host exchange of a newly emerging genus of the Paramyxoviridae, currently referred to as the unclassified morbillivirus-related viruses (UMRVs). In contrast to other genera of the Paramyxoviridae, where bats have been shown to be a key host species, we show that rodents (and, in particular, Rattus rattus) are significant spreaders of UMRVs. We predict that the ecological particularities of the southwestern Indian Ocean, where small mammal species often live in densely packed, multispecies communities, in combination with the increasing invasion of R. rattus and perturbations of endemic animal communities by active anthropological development, will have a major influence on the dynamics of UMRV infection. IMPORTANCE: Identification of the infectious agents that circulate within wild animal reservoirs is essential for several reasons: (i) infectious disease outbreaks often originate from wild fauna; (ii) anthropological expansion increases the risk of contact between human and animal populations and, as a result, the risk of disease emergence; (iii) evaluation of pathogen reservoirs helps in elaborating preventive measures to limit the risk of disease emergence. Many paramyxoviruses for which bats and rodents serve as major reservoirs have demonstrated their potential to cause disease in humans and animals. In the context of the biodiversity hot spot of southwestern Indian Ocean islands and their rich endemic fauna, we show that highly diverse UMRVs exchange between various endemic animal species, and their dissemination likely is facilitated by the introduced Rattus rattus. Hence, many members of the Paramyxoviridae appear well adapted for the study of the viral phylodynamics that may be associated with disease emergence.

Rickettsia spp. in seabird ticks from western Indian Ocean islands, 2011-2012.

We found a diversity of Rickettsia spp. in seabird ticks from 6 tropical islands. The bacteria showed strong host specificity and sequence similarity with strains in other regions. Seabird ticks may be key reservoirs for pathogenic Rickettsia spp., and bird hosts may have a role in dispersing ticks and tick-associated infectious agents over large distances.

Massive infection of seabird ticks with bacterial species related to Coxiella burnetii.

Seabird ticks are known reservoirs of bacterial pathogens of medical importance; however, ticks parasitizing tropical seabirds have received less attention than their counterparts from temperate and subpolar regions. Recently, Rickettsia africae was described to infect seabird ticks of the western Indian Ocean and New Caledonia, constituting the only available data on bacterial pathogens associated with tropical seabird tick species. Here, we combined a pyrosequencing-based approach with a classical molecular analysis targeting bacteria of potential medical importance in order to describe the bacterial community in two tropical seabird ticks, Amblyomma loculosum and Carios (Ornithodoros) capensis. We also investigated the patterns of prevalence and host specificity within the biogeographical context of the western Indian Ocean islands. The bacterial community of the two tick species was characterized by a strong dominance of Coxiella and Rickettsia. Our data support a strict Coxiella-host tick specificity, a pattern resembling the one found for Rickettsia spp. in the same two seabird tick species. Both the high prevalence and stringent host tick specificity suggest that these bacteria may be tick symbionts with probable vertical transmission. Detailed studies of the pathogenicity of these bacteria will now be required to determine whether horizontal transmission can occur and to clarify their status as potential human pathogens. More generally, our results show that the combination of next generation sequencing with targeted detection/genotyping approaches proves to be efficient in poorly investigated fields where research can be considered to be starting from scratch.

Tracing the colonization and diversification of the worldwide seabird ectoparasite Ixodes uriae.

Historical patterns of dispersal and population isolation are key components shaping contemporary genetic diversity across landscapes and require explicit consideration when examining the relative role of different factors in driving the evolution of host specificity in parasitic organisms. In this study, we investigate the worldwide colonization history of a common ectoparasite of seabirds, the tick Ixodes uriae. This tick has a circumpolar distribution across both hemispheres but has repeatedly formed host-specific races within different regions. By combining mitochondrial and nuclear data, we infer how this species spread to its present-day distribution and how the colonization process may have affected the geographic and host-associated structure of this tick within regions. We demonstrate that I. uriae is highly structured at a global scale and isolates into four genetic groups that correspond to well-defined geographical regions. Molecular dating suggests that the diversification of I. uriae began in the early Miocene (22 Myr) and that this tick colonized most of the southern hemisphere before moving into northern latitudes via two independent routes. However, no relationship between the degree of host race divergence and colonization history was evident, supporting previous hypotheses that host specialization evolves relatively rapidly in this parasite, but does not typically lead to speciation. We discuss the possible historical and contemporary mechanisms of large-scale dispersal for this ectoparasite and how its biological characteristics may condition current patterns of genetic diversity. More generally, our results illustrate how combining broad-scale sampling and modern molecular tools can help disentangle complex patterns of diversification in widespread parasites.

Diversification of an emerging pathogen in a biodiversity hotspot: Leptospira in endemic small mammals of Madagascar.

Biodiversity hotspots and associated endemism are ideal systems for the study of parasite diversity within host communities. Here, we investigated the ecological and evolutionary forces acting on the diversification of an emerging bacterial pathogen, Leptospira spp., in communities of endemic Malagasy small mammals. We determined the infection rate with pathogenic Leptospira in 20 species of sympatric rodents (subfamily Nesomyinae) and tenrecids (family Tenrecidae) at two eastern humid forest localities. A multilocus genotyping analysis allowed the characterization of bacterial diversity within small mammals and gave insights into their genetic relationships with Leptospira infecting endemic Malagasy bats (family Miniopteridae and Vespertilionidae). We report for the first time the presence of pathogenic Leptospira in Malagasy endemic small mammals, with an overall prevalence of 13%. In addition, these hosts harbour species of Leptospira (L. kirschneri, L. borgpetersenii and L. borgpetersenii group B) which are different from those reported in introduced rats (L. interrogans) on Madagascar. The diversification of Leptospira on Madagascar can be traced millions of years into evolutionary history, resulting in the divergence of endemic lineages and strong host specificity. These observations are discussed in relation to the relative roles of endemic vs. introduced mammal species in the evolution and epidemiology of Leptospira on Madagascar, specifically how biodiversity and biogeographical processes can shape community ecology of an emerging pathogen and lead to its diversification within native animal communities.

An experimental test of host specialization in a ubiquitous polar ectoparasite: a role for adaptation?

The evolution of host specificity is considered to be an essential mechanism driving parasite diversity. It may be governed by adaptive constraints that lead to host-dependent fitness trade-offs. Alternatively, specificity may arise via transmission constraints that isolate parasite populations, without necessarily involving adaptation per se. Here, we ask whether the repeated observation of host-associated genetic races across the worldwide distribution of the seabird ectoparasite Ixodes uriae is associated with host adaptation. We conducted a field-based experiment to test for adaptive specialisation in host races of I. uriae. We transferred unengorged ticks of two life stages (nymphs and adults) originating from three host species (black-legged kittiwake, common guillemot and Atlantic puffin) onto young kittiwake nestlings and followed attraction and attachment rates, engorgement times and feeding success of the transplanted ticks. All ticks were also typed genetically to match exploitation patterns with genetic differences among races. Ticks from atypical hosts were significantly less attracted to nestlings than ticks from the typical host, and showed lower feeding success and higher mortality. The degree of host specificity matched patterns of neutral genetic variation among races, with puffin ticks being more specific than guillemot ticks. Differences in specificity were also apparent among tick life stages, suggesting that nymphal ticks may be less discriminating of host type than adult ticks. Our results indicate that the genetic divergence previously observed among sympatric I. uriae host races is at least partially linked to adaptive specialisation to the host species and not simply to host-mediated transmission. They also suggest that the adaptation process may evolve differently in different life stages based on trade-offs with physiological constraints. The identification of the selective forces acting in host specialization will now be necessary to better characterize these patterns and to understand how transmission interacts with the adaptation process to generate parasite biodiversity.

Viral maintenance and excretion dynamics of coronaviruses within an Egyptian rousette fruit bat maternal colony: considerations for spillover.

Novel coronavirus species of public health and veterinary importance have emerged in the first two decades of the twenty-first century, with bats identified as natural hosts for progenitors of many coronaviruses. Targeted wildlife surveillance is needed to identify the factors involved in viral perpetuation within natural host populations, and drivers of interspecies transmission. We monitored a natural colony of Egyptian rousette bats at monthly intervals across two years to identify circulating coronaviruses, and to investigate shedding dynamics and viral maintenance within the colony. Three distinct lineages were detected, with different seasonal temporal excretion dynamics. For two lineages, the highest periods of coronavirus shedding were at the start of the year, when large numbers of bats were found in the colony. Highest peaks for a third lineage were observed towards the middle of the year. Among individual bat-level factors (age, sex, reproductive status, and forearm mass index), only reproductive status showed significant effects on excretion probability, with reproductive adults having lower rates of detection, though factors were highly interdependent. Analysis of recaptured bats suggests that viral clearance may occur within one month. These findings may be implemented in the development of risk reduction strategies for potential zoonotic coronavirus transmission.

Migratory patterns of two major influenza virus host species on tropical islands.

Animal migration is a major driver of infectious agent dispersal. Duck and seabird migrations, for instance, play a key role in the spatial transmission dynamics and gene flow of avian influenza viruses (AIV), worldwide. On tropical islands, brown and lesser noddies (Anous stolidus and Anous tenuirostris) may be important AIV hosts, but the lack of knowledge on their migratory behaviour limits our understanding of virus circulation in island networks. Here we show that high connectivity between islands generated by non-breeding dispersive behaviours may be a major driver in the spread and the maintenance of AIV among tropical islands of the western Indian Ocean. Tracking data highlight two types of dispersive behaviours during the non-breeding season: birds either staying in the vicinity of their breeding ground (on Bird Island, Seychelles), or moving to and roosting on other islands in the western Indian Ocean. Migrant birds used a wide range of roosting places from the Tanzanian coasts to the Maldives archipelago and Tromelin Island. Epidemiological data confirm that brown and lesser noddies are major hosts for AIV, although significant variations of seroprevalence between species suggest that other biological and ecological drivers could be involved in virus infection and transmission dynamics.

A population in perpetual motion: Highly dynamic roosting behavior of a tropical island endemic bat.

Although island endemic bats are a source of considerable conservation concerns, their biology remains poorly known. Here, we studied the phenology and roosting behavior of a tropical island endemic species: the Reunion free-tailed bat (Mormopterus francoismoutoui). This widespread and abundant species occupies various natural and anthropogenic environments such as caves and buildings. We set up fine-scale monitoring of 19 roosts over 27 months in Reunion Island and analyzed roost size and composition, sexual and age-associated segregation of individuals, as well as the reproductive phenology and body condition of individuals. Based on extensive data collected from 6721 individuals, we revealed a highly dynamic roosting behavior, with marked seasonal sex-ratio variation, linked to distinct patterns of sexual aggregation among roosts. Despite the widespread presence of pregnant females all over the island, parturition was localized in a few roosts, and flying juveniles dispersed rapidly toward all studied roosts. Our data also suggested a 7-month delay between mating and pregnancy, highlighting a likely long interruption of the reproductive cycle in this tropical bat. Altogether, our results suggest a complex social organization in the Reunion free-tailed bat, with important sex-specific seasonal and spatial movements, including the possibility of altitudinal migration. Bat tracking and genetic studies would provide additional insights into the behavioral strategies that shape the biology of this enigmatic bat species. The fine-scale spatiotemporal data revealed by our study will serve to the delineation of effective conservation plans, especially in the context of growing urbanization and agriculture expansion in Reunion Island.

Interaction between Old World fruit bats and humans: From large scale ecosystem services to zoonotic diseases.

The Old World tropical and subtropical frugivorous bat genus Rousettus (Pteropodidae) contains species with broad distributions, as well as those occurring in restricted geographical areas, particularly islands. Herein we review the role of Rousettus as a keystone species from a global "One Health" approach and related to ecosystem functioning, zoonotic disease and public health. Rousettus are efficient at dispersing seeds and pollinating flowers; their role in forest regeneration is related to their ability to fly considerable distances during nightly foraging bouts and their relatively small body size, which allows them to access fruits in forested areas with closed vegetation. Rousettus are also reservoirs for various groups of pathogens (viruses, bacteria, fungi, protozoa), which, by definition, are infectious agents causing disease. The study of day roosts of different species of Rousettus and the successful establishment of captive breeding colonies have provided important details related to the infection dynamics of their associated pathogens. Large-scale conversion of forested areas into agricultural landscapes has increased contact between humans and Rousettus, therefore augmenting the chances of infectious agent spillover. Many crucial scientific details are still lacking related to members of this genus, which have direct bearing on the prevention of emerging disease outbreaks, as well as the conservation of these bats. The public should be better informed on the capacity of fruit bats as keystone species for large scale forest regeneration and in spreading pathogens. Precise details on the transmission of zoonotic diseases of public health importance associated with Rousettus should be given high priority.

Seasonality of coronavirus shedding in tropical bats.

Anticipating cross-species transmission of zoonotic diseases requires an understanding of pathogen infection dynamics within natural reservoir hosts. Although bats might be a source of coronaviruses (CoVs) for humans, the drivers of infection dynamics in bat populations have received limited attention. We conducted a fine-scale 2-year longitudinal study of CoV infection dynamics in the largest colony of Reunion free-tailed bats (Mormopterus francoismoutoui), a tropical insectivorous species. Real-time PCR screening of 1080 fresh individual faeces samples collected during the two consecutive years revealed an extreme variation of the detection rate of bats shedding viruses over the birthing season (from 0% to 80%). Shedding pulses were repeatedly observed and occurred both during late pregnancy and within two months after parturition. An additional shedding pulse at the end of the second year suggests some inter-annual variations. We also detected viral RNA in bat guano up to three months after bats had left the cave. Our results highlight the importance of fine-scale longitudinal studies to capture the rapid change of bat CoV infection over months, and that CoV shedding pulses in bats may increase spillover risk.

Seasonal shedding patterns of diverse henipavirus-related paramyxoviruses in Egyptian rousette bats.

Bat-borne viruses in the Henipavirus genus have been associated with zoonotic diseases of high morbidity and mortality in Asia and Australia. In Africa, the Egyptian rousette bat species (Rousettus aegyptiacus) is an important viral host in which Henipavirus-related viral sequences have previously been identified. We expanded these findings by assessing the viral dynamics in a southern African bat population. A longitudinal study of henipavirus diversity and excretion dynamics identified 18 putative viral species circulating in a local population, three with differing seasonal dynamics, and the winter and spring periods posing a higher risk of virus spillover and transmission. The annual peaks in virus excretion are most likely driven by subadults and may be linked to the waning of maternal immunity and recolonization of the roost in early spring. These results provide insightful information into the bat-host relationship that can be extrapolated to other populations across Africa and be communicated to at-risk communities as a part of evidence-based public health education and prevention measures against pathogen spillover threats.

Avian influenza circulation in the Camargue (south of France) during the 2006-07 season.

Situated at the crossroads of numerous migratory routes of Palaearctic birds, the Camargue is considered a high-risk area for the introduction and transmission of numerous avian-borne pathogens. We investigated the epidemiologic cycles of avian influenza viruses (AIVs) in the local bird community by performing regular sampling on a large variety of bird species during 11 consecutive months in 2006-07. To detect the presence of AIV, SYBR green reverse transcriptase-PCR targeting the M gene was performed on 2901 samples from 66 bird species. A clear seasonal pattern of AIV circulation in ducks was observed during autumn and winter, with higher prevalence rates in early fall. Our results also support an absence of circulation of AIV in passerine birds during spring and the wintering periods. Finally, even if the prevalence of infection was very low, AIVs were found in gulls in breeding colonies, indicating a possible specific circulation in spring in these birds.