Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum

Alison J. Peel [et al.]Bats, including African straw-coloured fruit bats (Eidolon helvum), have been highlighted as reservoirs of many recently emerged zoonotic viruses. This common, widespread and ecologically important species was the focus of longitudinal and continent-wide studies of the epidemiological and ecology of Lagos bat virus, henipaviruses and Achimota viruses. Here we present a spatial, morphological, demographic, genetic and serological dataset encompassing 2827 bats from nine countries over an 8-year period. Genetic data comprises cytochrome b mitochondrial sequences (n=608) and microsatellite genotypes from 18 loci (n=544). Tooth-cementum analyses (n=316) allowed derivation of rare age-specific serologic data for a lyssavirus, a henipavirus and two rubulaviruses. This dataset contributes a substantial volume of data on the ecology of E. helvum and its viruses and will be valuable for a wide range of studies, including viral transmission dynamic modelling in age-structured populations, investigation of seasonal reproductive asynchrony in wide-ranging species, ecological niche modelling, inference of island colonisation history, exploration of relationships between island and body size, and various spatial analyses of demographic, morphometric or serological data.Peer Reviewe

The epidemiology of Lagos bat virus and henipaviruses in straw-coloured fruit bats (Eidolon helvum), using population genetics to infer population connectivity

The straw-coloured fruit bat, Eidolon helvum, has been identified as a reservoir for potentially-zoonotic henipaviruses and Lagos bat virus (LBV) in continental Africa. Longitudinal studies at a large urban colony in Accra, Ghana aim to better understand E. helvum and viral ecology, as well as the nature of human-bat interactions. To assess whether the findings from these studies can be extrapolated across the species’ continental range, more information on the movement ecology of the species and connectivity of populations across its range was required. A multifaceted approach, using techniques from the field of genetics, population ecology, and virology, was used to understand the ways in which the structure and dynamics of fruit bat populations across Africa may affect the viral transmission dynamics within them. Given recent difficulties in using electronic positioning systems on E. helvum to track movement, genetic methods were proposed as the most appropriate way to assess connectivity between populations across such a vast range. Henipavirus and LBV serological analyses were undertaken on samples from 12 populations of E. helvum bats across its continental and offshore-island range. A combination of mitochondrial DNA and microsatellite markers were used to describe the genetic metapopulation structure of E. helvum and data were obtained in each location on population sizes, demographic structure, reproductive and migratory seasonality, as well as bat-human interactions. Consistent with expectations for a vagile migratory species, a panmictic continental population structure was detected across its continental range, although the extent of this panmixia was greater than previously detected in any other mammal or bird. Antibodies to henipaviruses and LBV were detected in all continental populations. Isolated island populations in the Gulf of Guinea were genetically distinct from each other and the continental population. Given the isolation of these island fruit bats and the lack of connectivity with other populations, it was expected that populations would be too small to allow persistence of any viruses that cause acute, immunising infections. Contrary to expectations, island individuals displayed evidence for exposure to both viruses. E. helvum is known to roost close in proximity to human populations across continental Africa, and these results could therefore have important public health implications. Further longitudinal studies across multiple locations and information on social structure, daily and seasonal movements are needed to make inferences about virus transmission dynamics and zoonotic risks within the complex population structure.I would like to acknowledge the funders of this research, including the Cambridge Infectious Diseases Consortium (originally funded by the Veterinary Training and Research Initiative), Charles Slater Fund, Jowett Fund, Society of General Microbiology, Daisy Balogh Grant, Wolfson College, and the Zebra Foundation for Veterinary Zoological Educatio

The implementation of a shared reading programme within a university : a case study

Based on research into the benefits of involvement in reading for pleasure and the operation in the US of pre-arrival shared reading schemes for those about to embark on a university education, both within the context of wider research into how to engage newly arrived students in their institution, an exploration was made of the likely response to such a shared reading scheme within a London university. A representative sample of current first years were asked about their how they spent their leisure time, their attitudes towards and involvement in reading for pleasure and their reactions to such a potential scheme. The findings were that more reading for pleasure was taking part than had been anticipated, that students were generally keen to become more involved in reading and that a shared reading scheme would be welcomed by the majority of students. The decisions made on the basis of the outcomes are discussed, along with recommendations for future associated research

Keeping the conversation going: How progressivity is prioritised in co-remembering talk between couples impacted by dementia

This article explores how partners keep the conversation going with people living with dementia (PLWD) when speaking about shared memories. Remembering is important for PLWD and their families. Indeed, memory loss is often equated with identity loss. In conversation, references to shared past events (co-rememberings) can occasion interactional trouble if memories cannot be mutually recalled. This article analyses partners’ interactional practices that enable progressivity in conversations about shared memories with a PLWD. In previous research, both informal and formal carers have reported that they can find interacting with PLWD difficult. Identifying practices used by partners is one way to begin addressing those difficulties. Analytical findings are based on over 26 hours of video data from domestic settings where partners have recorded their interactions with their spouse/close friend who is living with dementia. The focus is on 14 sequences of conversation about shared memories. We show how particular practices (candidate answers, tag questions and single-party memory of a shared event) structure the interaction to facilitate conversational progression. When partners facilitate conversational progressivity, PLWD are less likely to experience stalls in conversation. Our findings suggest the actual recall of memory is less relevant than the sense of shared connection resulting from the conversational activity of co-remembering, aiding maintenance of individual and shared identities. These findings have relevance for wider care settings

'If I do 10-15 normal deliveries in a month I hardly ever sleep at home.' A qualitative study of health providers' reasons for high rates of caesarean deliveries in private sector maternity care in Delhi, India.

BACKGROUND: Although the overall rate of caesarean deliveries in India remains low, rates are higher in private than in public facilities. In a household survey in Delhi, for instance, more than half of women delivering in private facilities reported a caesarean section. Evidence suggests that not all caesarean sections are clinically necessary and may even increase morbidity. We present providers' perspectives of the reasons behind the high rates of caesarean births in private facilities, and possible solutions to counter the trend. METHODS: Fourteen in-depth interviews were conducted with high-end private sector obstetricians and other allied providers in Delhi and its neighbouring cities, Gurgaon and Ghaziabad. RESULTS: Respondents were of the common view that private sector caesarean rates were unreasonably high and perceived time and doctors' convenience as the foremost reasons. Financial incentives had an indirect effect on decision-making. Obstetricians felt that they must maintain high patient loads to be commercially successful. Many alluded to their busy working lives, which made it challenging for them to monitor every delivery individually. Besides fearing for patient safety in these situations, they were fearful of legal action if anything went wrong. A lack of context specific guidelines and inadequate support from junior staff and nurses exacerbated these problems. Maternal demand also played a role, as the consumer-provider relationship in private healthcare incentivised obstetricians to fulfil patient demands for caesarean section. Suggested solutions included more support, from either well-trained midwives and junior staff or using a 'shared practice' model; guidelines introduced by an Indian body; increased regulation within the sector and public disclosure of providers' caesarean rates. CONCLUSIONS: Commercial interests contribute indirectly to high caesarean rates, as solo obstetricians juggle the need to maintain high patient loads with inadequate support staff. Perceptions amongst providers and consumers of caesarean section as the 'safe' option have re-defined caesareans as the new 'normal', even for low-risk deliveries. At the policy level, guidelines and public disclosures, strong initiatives to develop professional midwifery, and increasing public awareness, could bring about a sustainable reduction in the present high rates

Risk of SARS-CoV-2 transmission from humans to bats : an Australian assessment

SARS-CoV-2, the cause of COVID-19, infected over 100 million people globally by February 2021. Reverse zoonotic transmission of SARS-CoV-2 from humans to other species has been documented in pet cats and dogs, big cats and gorillas in zoos, and farmed mink. As SARS-CoV-2 is closely related to known bat viruses, assessment of the potential risk of transmission of the virus from humans to bats, and its subsequent impacts on conservation and public health, is warranted. A qualitative risk assessment was conducted by a multi-disciplinary group to assess this risk in bats in the Australian context, with the aim of informing risk management strategies for human activities involving interactions with bats. The overall risk of SARS-CoV-2 establishing in an Australian bat population was assessed to be Low, however with a High level of uncertainty. The outcome of the assessment indicates that, for the Australian situation where the prevalence of COVID-19 in humans is very low, it is reasonable for research and rehabilitation of bats to continue, provided additional biosecurity measures are applied. Risk assessment is challenging for an emerging disease where information is lacking and the situation is changing rapidly; assessments should be revised if human prevalence or other important factors change significantly. The framework developed here, based on established animal disease risk assessment approaches adapted to assess reverse zoonotic transmission, has potential application to a range of wildlife species and situations

Estimating viral prevalence with data fusion for adaptive two-phase pooled sampling.

The COVID-19 pandemic has highlighted the importance of efficient sampling strategies and statistical methods for monitoring infection prevalence, both in humans and in reservoir hosts. Pooled testing can be an efficient tool for learning pathogen prevalence in a population. Typically, pooled testing requires a second-phase retesting procedure to identify infected individuals, but when the goal is solely to learn prevalence in a population, such as a reservoir host, there are more efficient methods for allocating the second-phase samples.To estimate pathogen prevalence in a population, this manuscript presents an approach for data fusion with two-phased testing of pooled samples that allows more efficient estimation of prevalence with less samples than traditional methods. The first phase uses pooled samples to estimate the population prevalence and inform efficient strategies for the second phase. To combine information from both phases, we introduce a Bayesian data fusion procedure that combines pooled samples with individual samples for joint inferences about the population prevalence.Data fusion procedures result in more efficient estimation of prevalence than traditional procedures that only use individual samples or a single phase of pooled sampling.The manuscript presents guidance on implementing the first-phase and second-phase sampling plans using data fusion. Such methods can be used to assess the risk of pathogen spillover from reservoir hosts to humans, or to track pathogens such as SARS-CoV-2 in populations

Transmission or within-host dynamics driving pulses of zoonotic viruses in reservoir-host populations

Progress in combatting zoonoses that emerge from wildlife is often constrained by limited knowledge of the biology of pathogens within reservoir hosts. We focus on the host–pathogen dynamics of four emerging viruses associated with bats: Hendra, Nipah, Ebola, and Marburg viruses. Spillover of bat infections to humans and domestic animals often coincides with pulses of viral excretion within bat populations, but the mechanisms driving such pulses are unclear. Three hypotheses dominate current research on these emerging bat infections. First, pulses of viral excretion could reflect seasonal epidemic cycles driven by natural variations in population densities and contact rates among hosts. If lifelong immunity follows recovery, viruses may disappear locally but persist globally through migration; in either case, new outbreaks occur once births replenish the susceptible pool. Second, epidemic cycles could be the result of waning immunity within bats, allowing local circulation of viruses through oscillating herd immunity. Third, pulses could be generated by episodic shedding from persistently infected bats through a combination of physiological and ecological factors. The three scenarios can yield similar patterns in epidemiological surveys, but strategies to predict or manage spillover risk resulting from each scenario will be different. We outline an agenda for research on viruses emerging from bats that would allow for differentiation among the scenarios and inform development of evidence-based interventions to limit threats to human and animal health. These concepts and methods are applicable to a wide range of pathogens that affect humans, domestic animals, and wildlife

Transmission or Within-Host Dynamics Driving Pulses of Zoonotic Viruses in Reservoir-Host Populations.

Progress in combatting zoonoses that emerge from wildlife is often constrained by limited knowledge of the biology of pathogens within reservoir hosts. We focus on the host-pathogen dynamics of four emerging viruses associated with bats: Hendra, Nipah, Ebola, and Marburg viruses. Spillover of bat infections to humans and domestic animals often coincides with pulses of viral excretion within bat populations, but the mechanisms driving such pulses are unclear. Three hypotheses dominate current research on these emerging bat infections. First, pulses of viral excretion could reflect seasonal epidemic cycles driven by natural variations in population densities and contact rates among hosts. If lifelong immunity follows recovery, viruses may disappear locally but persist globally through migration; in either case, new outbreaks occur once births replenish the susceptible pool. Second, epidemic cycles could be the result of waning immunity within bats, allowing local circulation of viruses through oscillating herd immunity. Third, pulses could be generated by episodic shedding from persistently infected bats through a combination of physiological and ecological factors. The three scenarios can yield similar patterns in epidemiological surveys, but strategies to predict or manage spillover risk resulting from each scenario will be different. We outline an agenda for research on viruses emerging from bats that would allow for differentiation among the scenarios and inform development of evidence-based interventions to limit threats to human and animal health. These concepts and methods are applicable to a wide range of pathogens that affect humans, domestic animals, and wildlife.National Institutes of HealthThis is the author accepted manuscript. It is currently under an indefinite embargo pending publication by the Public Library of Science

Antigenic and genetic characterization of a divergent African virus, Ikoma lyssavirus

In 2009, a novel lyssavirus (subsequently named Ikoma lyssavirus, IKOV) was detected in the brain of an African civet (Civettictis civetta) with clinical rabies in the Serengeti National Park of Tanzania. The degree of nucleotide divergence between the genome of IKOV and those of other lyssaviruses predicted antigenic distinction from, and lack of protection provided by, available rabies vaccines. In addition, the index case was considered likely to be an incidental spillover event, and therefore the true reservoir of IKOV remained to be identified. The advent of sensitive molecular techniques has led to a rapid increase in the discovery of novel viruses. Detecting viral sequence alone, however, only allows for prediction of phenotypic characteristics and not their measurement. In the present study we describe the in vitro and in vivo characterization of IKOV, demonstrating that it is (1) pathogenic by peripheral inoculation in an animal model, (2) antigenically distinct from current rabies vaccine strains and (3) poorly neutralized by sera from humans and animals immunized against rabies. In a laboratory mouse model, no protection was elicited by a licensed rabies vaccine. We also investigated the role of bats as reservoirs of IKOV. We found no evidence for infection among 483 individuals of at least 13 bat species sampled across sites in the Serengeti and Southern Kenya