Detection, characterization, and phylogenetic analysis of a near-whole genome sequence of a novel astrovirus in an endemic Malagasy fruit bat, Rousettus madagascariensis

Bats (order: Chiroptera ) are known to host a diverse range of viruses, some of which present a public health risk. Thorough viral surveillance is therefore essential to predict and potentially mitigate zoonotic spillover. Astroviruses (family: Astroviridae ) are an understudied group of viruses with a growing amount of indirect evidence for zoonotic transfer. Astroviruses have been detected in bats with significant prevalence and diversity, suggesting that bats may act as important astrovirus hosts. Most astrovirus surveillance in wild bat hosts has, to date, been restricted to single-gene PCR detection and concomitant Sanger sequencing; additionally, many bat species and many geographic regions have not yet been surveyed for astroviruses at all. Here, we use metagenomic Next Generation Sequencing (mNGS) to detect astroviruses in three species of Madagascar fruit bats, Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis . We detect numerous partial sequences from all three species and one near-full length astrovirus sequence from Rousettus madagascariensis , which we use to characterize the evolutionary history of astroviruses both within bats and the broader mammalian clade, Mamastrovirus . Taken together, applications of mNGS implicate bats as important astrovirus hosts and demonstrate novel patterns of bat astrovirus evolutionary history, particularly in the Southwest Indian Ocean region.

Finding food in the hunger season: A mixed methods approach to understanding wild plant foods in relation to food security and dietary diversity in southeastern Madagascar

In many rural farming societies, wild plant foods (WPFs) continue to play an important role in everyday diets as well as in coping with hunger during food shortages. However, WPF collection and consumption may pose challenges to biodiversity conservation efforts (e.g., in protected areas), and some “famine foods,” foods not typically eaten under normal conditions, may have deleterious health impacts. Using data from a cross-sectional survey of 328 smallholder farmers and fisherfolk living in 15 villages surrounding Manombo Special Reserve on the southeastern coast of Madagascar, we examine the relationship between food security, dietary diversity, and consumption of WPFs, specifically giant aquatic arrowhead or via (Typhonodorum lindleyanum) and Polynesian arrowroot or tavolo (Tacca leontopetaloides), during the region's main lean season. We complement survey findings with focus group interviews to document traditional ecological knowledge and perceptions of these WPFs, including how tavolo and via are rendered edible, as well as human health effects from collecting, preparing, and eating them. Using multilevel logistic regression modeling, we found that consumption of these WPFs were significantly associated with inadequate nutrition among farmers. Wealthier households were less likely to consume these WPFs as a coping strategy during food insecure periods, while larger and more food insecure households were more likely to consume them. These findings reaffirm the importance of access to natural areas and support the design of protected area conservation strategies that honor local foodways and consider WPFs that serve as food safety nets for more vulnerable populations.

Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade

Bats are natural reservoirs for both Alpha- and Betacoronaviruses and the hypothesized original hosts of five of seven known zoonotic coronaviruses. To date, the vast majority of bat coronavirus research has been concentrated in Asia, though coronaviruses are globally distributed; indeed, SARS-CoV and SARS-CoV-2-related Betacoronaviruses in the subgenus Sarbecovirus have been identified circulating in Rhinolophid bats in both Africa and Europe, despite the relative dearth of surveillance in these regions. As part of a long-term study examining the dynamics of potentially zoonotic viruses in three species of endemic Madagascar fruit bat (Pteropus rufus, Eidolon dupreanum, Rousettus madagascariensis), we carried out metagenomic Next Generation Sequencing (mNGS) on urine, throat, and fecal samples obtained from wild-caught individuals. We report detection of RNA derived from Betacoronavirus subgenus Nobecovirus in fecal samples from all three species and describe full genome sequences of novel Nobecoviruses in P. rufus and R. madagascariensis. Phylogenetic analysis indicates the existence of five distinct Nobecovirus clades, one of which is defined by the highly divergent ancestral sequence reported here from P. rufus bats. Madagascar Nobecoviruses derived from P. rufus and R. madagascariensis demonstrate, respectively, Asian and African phylogeographic origins, mirroring those of their fruit bat hosts. Bootscan recombination analysis indicates significant selection has taken place in the spike, nucleocapsid, and NS7 accessory protein regions of the genome for viruses derived from both bat hosts. Madagascar offers a unique phylogeographic nexus of bats and viruses with both Asian and African phylogeographic origins, providing opportunities for unprecedented mixing of viral groups and, potentially, recombination. As fruit bats are handled and consumed widely across Madagascar for subsistence, understanding the landscape of potentially zoonotic coronavirus circulation is essential for mitigation of future zoonotic threats.

Bushpig (Potamochoerus larvatus) Hunting in Rural Areas of Madagascar and Its Health and Socioeconomic Implications

Bushmeat consumption and trade plays a relevant role in many tropical countries as a source of protein and income for rural populations. In Madagascar, rural populations depend heavily on natural resources and wildlife as source of income and protein. The bushpig (Potamochoerus larvatus) is the largest mammal available in the island and regularly hunted. However, little is known about the importance and characteristics of this activity and its implication as a potential source of pathogens for both humans and domestic animals. A cross-sectional study was conducted in 2014–2015 in five different regions of rural Madagascar suspected to have significant bushpig populations to (i) quantify and characterize the importance of bushpig hunting, (ii) assess the socioeconomic impact of bushpig trade, (iii) evaluate the potential pathogen transmission between bushpigs, domestic pigs and humans. A total of 77 hunters, 10 butchers and 95 pig farmers were individually interviewed. Hunting seasonality and the perception of local hunters with regards to the dynamics of bushpig populations in the last decade differed between the tropical dry and tropical sub-arid climatic zones. The top reason for hunting bushpigs was crop protection but personal consumption and selling of meat were also common. Hunting efficacy was largely dependent on the technique used. Snares and traps, the most widely used techniques, allowed the majority of hunters to catch from one to 10 bushpigs per year. Limited commercial bushpig trade was observed with only 0.8 bushpig sold in average per year and per hunter, representing a 16 USD income. The average price per kilo sold was USD 0.8 and the average profit received by each butcher/collector after the sale of a carcass was USD 11.9. No perception of disease risks nor precautions were taken to prevent potential pathogen transmission from bushpig to humans or pigs. Most of the hunters (68%) indicated that they had never seen a diseased bushpig. Bushpig hunting in our study areas in Madagascar was basically a small-scale subsistence hunting, very different from commercial bushmeat hunting described in areas of Central Africa or the Amazon Basin. More research is needed to verify the sustainability of bushpig hunting and its potential role in terms of reducing pressure on other endemic wildlife species and transmitting pathogens to humans and pigs.

Disparate roost sites drive intraspecific physiological variation in a Malagasy bat

Many species are widely distributed and individual populations can experience vastly different environmental conditions over seasonal and geographic scales. With such a broad ecological reality, datasets with limited spatial and temporal resolution may not accurately represent a species and could lead to poorly informed management decisions. Because physiological flexibility can help species tolerate environmental variation, we studied the physiological responses of two separate populations of Macronycteris commersoni, a bat widespread across Madagascar, in contrasting seasons. The populations roost under the following dissimilar conditions: either a hot, well-buffered cave or within open foliage, unprotected from the local weather. We found that flexible torpor patterns, used in response to prevailing ambient temperature and relative humidity, were central to keeping energy budgets balanced in both populations. While bats’ metabolic rate during torpor and rest did not differ between roosts, adjusting torpor frequency, duration and timing helped bats maintain body condition. Interestingly, the exposed forest roost induced extensive use of torpor, which exceeded the torpor frequency of overwintering bats that stayed in the cave for months and consequently minimised daytime resting energy expenditure in the forest. Our current understanding of intraspecific physiological variation is limited and physiological traits are often considered to be fixed. The results of our study therefore highlight the need for examining species at broad environmental scales to avoid underestimating a species’ full capacity for withstanding environmental variation, especially in the face of ongoing, disruptive human interference in natural habitats.

Understanding human-flying fox interactions in the Agusan Marsh Wildlife Sanctuary as basis for conservation policy interventions

There is no documented flying fox hunting study done in the Agusan Marsh Wildlife Sanctuary (AMWS) which is known to harbor many threatened wildlife species. The Large Flying Fox Pteropus vampyrus is known to be threatened by hunting in the AMWS despite existing laws, such as the Wildlife Act. We conducted semi-structured interviews from September 2017 to January 2018 with 240 hunters in 10 villages through purposive sampling to determine the socio-demographic and economic profile of the hunters, their conservation awareness, perceptions on the monitoring scheme and enforcement, possible hunting patterns, and hunting drivers. Results showed that farming and fishing are the most common livelihoods of hunters. Most hunters achieved an education at the elementary level (42.9%), and belong to a household with 4–6 members (55.5%), often with only one member having a meager daily income (80.7%). Annual flooding was the main economic constraint to the hunters. Largely comprised of indigenous Manobos (62.9%), the majority of hunters did not believe in avoiding taboo species (85.4%). Most of the hunters were unaware of laws protecting Wildlife (62.9%) and unable to differentiate between threatened and non-threatened species (86.3%). Poor implementation of the monitoring scheme and insufficient enforcement were also observed in AMWS. Kites with hooks (55%) and guns (31.7%) were used to hunt P. vampyrus mostly for local consumption (83.3%). Multivariate analysis revealed that daily income and engagement in conservation negatively affected hunting intensity. With many constraints in totally banning hunting in poor and wildlife-dependent indigenous communities in AMWS, flexible policies must be considered. It is more reasonable and realistic to consider science-based hunting quotas in policy interventions to balance conservation and human welfare. Positive behavioral change towards sustainable hunting and trading bans requires a combination of effective education campaigns, engagement of indigenous communities in conservation, improved enforcement, and sustainable livelihood programs.

Overview of Bat and Wildlife Coronavirus Surveillance in Africa: A Framework for Global Investigations

The ongoing coronavirus disease 2019 (COVID-19) pandemic has had devastating health and socio-economic impacts. Human activities, especially at the wildlife interphase, are at the core of forces driving the emergence of new viral agents. Global surveillance activities have identified bats as the natural hosts of diverse coronaviruses, with other domestic and wildlife animal species possibly acting as intermediate or spillover hosts. The African continent is confronted by several factors that challenge prevention and response to novel disease emergences, such as high species diversity, inadequate health systems, and drastic social and ecosystem changes. We reviewed published animal coronavirus surveillance studies conducted in Africa, specifically summarizing surveillance approaches, species numbers tested, and findings. Far more surveillance has been initiated among bat populations than other wildlife and domestic animals, with nearly 26,000 bat individuals tested. Though coronaviruses have been identified from approximately 7% of the total bats tested, surveillance among other animals identified coronaviruses in less than 1%. In addition to a large undescribed diversity, sequences related to four of the seven human coronaviruses have been reported from African bats. The review highlights research gaps and the disparity in surveillance efforts between different animal groups (particularly potential spillover hosts) and concludes with proposed strategies for improved future biosurveillance.

The Critical Importance of Old World Fruit Bats for Healthy Ecosystems and Economies

Despite extensive documentation of the ecological and economic importance of Old World fruit bats (Chiroptera: Pteropodidae) and the many threats they face from humans, negative attitudes towards pteropodids have persisted, fuelled by perceptions of bats as being pests and undesirable neighbours. Such long-term negativity towards bats is now further exacerbated by more recent disease-related concerns, particularly associated with the current COVID-19 pandemic. There remains an urgent need to investigate and highlight the positive and beneficial aspects of bats across the Old World. While previous reviews have summarised these extensively, numerous new studies conducted over the last 36 years have provided further valuable data and insights which warrant an updated review. Here we synthesise research on pteropodid-plant interactions, comprising diet, ecological roles, and ecosystem services, conducted during 1985-2020. We uncovered a total of 311 studies covering 75 out of the known 201 pteropodid species (37%), conducted in 47 countries. The majority of studies documented diet (52% of all studies; 67 pteropodid species), followed by foraging movement (49%; 50 pteropodid species), with fewer studies directly investigating the roles played by pteropodids in seed dispersal (24%; 41 pteropodid species), pollination (14%; 19 pteropodid species), and conflict with fruit growers (12%; 11 pteropodid species). Pteropodids were recorded feeding on 1072 plant species from 493 genera and 148 families, with fruits comprising the majority of plant parts consumed, followed by flowers/nectar/pollen, leaves, and other miscellaneous parts. Sixteen pteropodid species have been confirmed to act as pollinators for a total of 21 plant species, and 29 pteropodid species have been confirmed to act as seed dispersers for a total of 311 plant species. Anthropogenic threats disrupting bat-plant interactions in the Old World include hunting, direct persecution, habitat loss/disturbance, invasive species, and climate change, leading to ecosystem-level repercussions. We identify notable research gaps and important research priorities to support conservation action for pteropodids.

Understanding the Community Perceptions and Knowledge of Bats and Transmission of Nipah Virus in Bangladesh

Simple Summary

We assessed people’s knowledge, attitudes, and perceptions regarding bat ecology, myths associated with bats, and their involvement in the transmission of Nipah virus (NiV). We found that community people in Bangladesh had inadequate knowledge of bat ecology and myths surrounding NiV. People’s demographic characteristics, such as sex, age, occupation, level of education, and exposure to a Nipah outbreak, were determined to be key factors influencing their knowledge, attitudes, and perceptions of bat ecology, myths, and their transmission of NiV. Educational interventions are recommended for targeted groups in the community to raise awareness and to improve people’s current knowledge of the role of bats in ecosystem services and their risky behavioral practices driving NiV transmission in Bangladesh.

Abstract

Bats are known reservoirs of Nipah virus (NiV) and some filoviruses and also appear likely to harbor the evolutionary progenitors of severe acute respiratory syndrome coronavirus (SARS-CoV), severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), and Middle East respiratory syndrome coronavirus (MERS-CoV). While bats are considered a reservoir of deadly viruses, little is known about people’s knowledge, attitudes, and perceptions of bat conservation and ecology. The current study aimed to assess community people’s knowledge, attitudes, and perceptions of bat ecology, myths, and the role of bats in transmitting NiV in Bangladesh. Since 2001, NiV has been a continuous threat to public health with a mortality rate of approximately 70% in Bangladesh. Over the years, many public health interventions have been implemented to raise awareness about bats and the spreading of NiV among the community peoples of Nipah outbreak areas (NOAs) and Nipah non-outbreak areas (NNOAs). We hypothesized that people from both areas might have similar knowledge of bat ecology and myths about bats but different knowledge regarding their role in the spreading of NiV. Using a four-point Likert scale-based questionnaire, our analysis showed that most people lack adequate knowledge regarding the role of bats in maintaining the ecological balance and instead trust their beliefs in different myths about bats. Factor score analysis showed that respondents’ gender (p = 0.01), the outbreak status of the area (p = 0.03), and their occupation (p = 0.04) were significant factors influencing their knowledge of bat ecology and myths. A regression analysis showed that farmers had 0.34 times the odds of having correct or positive knowledge of bat ecology and myths than businesspersons (odds ratio (OR) = 0.34, 95% confidence interval (95% CI) = 0.15–0.78, p = 0.01). Regarding the spreading of NiV via bats, people had a lower level of knowledge. In NOAs, age (p = 0.00), occupation (p = 0.00), and level of education (p = 0.00) were found to be factors contributing to the amount of knowledge regarding the transmission of NiV, whereas in NNOAs, the contributing factors were occupation (p = 0.00) and level of education (p = 0.01). Regression analysis revealed that respondents who were engaged in services (OR = 3.02, 95% CI = 1.07–8.54, p = 0.04) and who had completed primary education (OR = 3.06, 95% CI = 1.02–9.17, p < 0.05) were likely to have correct knowledge regarding the spreading of NiV. Based on the study results, we recommend educational interventions for targeted groups in the community, highlighting the ecosystem services and conservation of bats so as to improve people’s current knowledge and subsequent behavior regarding the role of bats in ecology and the spreading of NiV in Bangladesh.

Characterization of ESBL-Producing Enterobacteria from Fruit Bats in an Unprotected Area of Makokou, Gabon

In Gabon, terrestrial mammals of protected areas have been identified as a possible source of antibiotic-resistant bacteria. Some studies on antibiotic resistance in bats have already been carried out. The main goal of our study was to detect extended-spectrum beta-lactamases (ESBLs) that are produced by enterobacteria from bats in the Makokou region in Gabon. Sixty-eight fecal samples were obtained from 68 bats caught in the forests located 1 km from the little town of Makokou. After culture and isolation, 66 Gram-negative bacterial colonies were obtained. The double-disk diffusion test confirmed the presence of ESBLs in six (20.69%) Escherichia coli isolates, four (13.79%) Klebsiella pneumoniae isolates, and one (3.45%) Enterobacter cloacae isolate. The analysis based on the nucleotide sequences of the ESBL resistance genes showed that all cefotaximase-Munichs (CTX-Ms) were CTX-M-15 and that all sulfhydryl variables (SHVs) were SHV-11: 41.67% CTX-M-15-producing E. coli, 16.67% CTX-M-15+SHV-11-producing E. coli, 8.33% CTX-M-15-producing K. pneumoniae, 25% CTX-M-15+SHV-11-producing K. pneumoniae, and 8.33% CTX-M-15-produced E. cloacae. This study shows for the first time the presence of multiresistant ESBL-producing enterobacteria in fruit bats in Makokou.

Emerging Foodborne and Agriculture-Related Viruses

Viruses rapidly evolve and can emerge in unpredictable ways. Transmission pathways by which foodborne viruses may enter human populations and evolutionary mechanisms by which viruses can become virulent are discussed in this chapter. A majority of viruses emerge from zoonotic animal reservoirs, often by adapting and infecting intermediate hosts, such as domestic animals and livestock. Viruses that are known foodborne threats include hepatitis E virus, tick-borne encephalitis virus, enteroviruses, adenovirus, and astroviruses, among others. Viruses may potentially evolve and emerge as a result of modern agricultural practices which can concentrate livestock and bring them into contact with wild animals. Examples of viruses that have emerged in this manner are influenza, coronaviruses such as severe acute respiratory syndrome and Middle East respiratory syndrome, and the Nipah virus. The role of bats, bush meat, rodents, pigs, cattle, and poultry as reservoirs from which infectious pathogenic viruses emerge are discussed.

Education to Action: Improving Public Perception of Bats

Public perception of bats has historically been largely negative with bats often portrayed as carriers of disease. Bats are commonly associated with vampire lore and thus elicit largely fearful reactions despite the fact that they are a vital and valuable part of the ecosystem. Bats provide a variety of essential services from pest control to plant pollination. Despite the benefits of bats to the environment and the economy, bats are suffering at the hands of humans. They are victims of turbines, human encroachment, pesticides, and, most recently, white nose syndrome. Because of their critical importance to the environment, humans should do what they can to help protect bats. We propose that humans will be more likely to do so if their perceptions and attitudes toward bats can be significantly improved. In a preliminary study we found some support for the idea that people can be educated about bats through bat oriented events and exhibits, and that this greater knowledge can inspire humans to act to save bats.