Hafaliana Christian Ranaivoson

Background: Bats are important reservoir hosts for a variety of microparasites, some of which are transmitted by ectoparasite vectors that include mites, fleas, lice, ticks, and bat flies (families Nycteribiidae and Streblidae). All of these ectoparasite taxa are known to parasitize two endemic fruit bats of Madagascar, Eidolon dupreanum and Rousettus madagascariensis. We aimed to describe the diversity of ectoparasite infestation for both bat species through morphological observation and DNA barcoding and elucidate ecological and climatic correlates of seasonal nycteribiid parasitism of these hosts. Methods: Live E. dupreanum and R. madagascariensis fruit bats were captured monthly in northern and central-eastern Madagascar from 2013-2020. Ectoparasites on all captured bats were counted and identified in the field, then collected into ethanol. Field identification of a subset of samples were confirmed via microscopy and DNA barcoding of the cytochrome C oxidase subunit 1 (COI) and 18S genes. The seasonal abundance of nycteribiid bat flies on both host bats was analyzed using generalized additive models, and the role of climate in driving this seasonality was assessed via cross-correlation analysis combined with generalized linear models. Phylogenetic trees were generated to compare COIand 18S sequences of Madagascar nycteribiid and streblid bat flies with available reference sequences from GenBank. Results: Ectoparasites corresponding to four broad taxa (mites, ticks, fleas, and bat flies) were recovered from 628 of 873 E. dupreanum and 831 of 862 R. madagascariensis . E. dupreanum were most commonly parasitized by Cyclopodia dubia nycteribiids and R. madagascariensis by Eucampsipoda madagascariensis nycteribiids or Megastrebla wenzeli streblids. We observed significant seasonality in nycteribiid abundance on both bat hosts, which varied by bat sex and was positively correlated with lagged temperature, precipitation, and humidity variables. Barcoding sequences recovered for all three bat fly species grouped with previously reported sequences, confirming morphological species identification. Our study contributes the first DNA barcodes of any kind reported for M. wenzeli and the first 18S barcodes for C. dubia . Conclusion: This study explores the diversity and abundance of ectoparasite burdens in two Malagasy fruit bat species, highlighting the importance of seasonal ecology and the influence of climate variables on parasitism, which correlates with resource availability.

Bats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. Picornavirales are an order of enteric viruses known to cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of Picornavirales worldwide. Divergent Caliciviridae and Picornaviridae (families within the Picornavirales ) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Bats live in close proximity to and are consumed widely as a food source by humans in Madagascar, providing opportunities for zoonotic transmission. Prior work in Madagascar has described numerous evolutionarily divergent bat viruses, some with zoonotic potential. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats ( Eidolon dupreanum , Pteropus rufus , and Rousettus madagascariensis ), we recovered 13 full-length and 37 partial-length genomic sequences within the order Picornavirales (36 Picornaviridae and 14 Caliciviridae sequences), which we identify and describe here. We find evidence that genetic exchange between mainland African bat and Madagascar bat Picornavirales likely shaped the diversification patterns of these novel sequences through recombination events between closely related Picornavirales ; thus far, high host fidelity appears to have limited these viruses from spilling over into other species.

Bats (Chiroptera) are a highly diverse mammalian order with over 1,500 species, roughly 200 of which are Old World Fruit Bats (family: Pteropodidae). Many pteropodid bats, especially those residing in seasonal environments, experience seasonal reproductive cycles, including discrete periods of gestation and lactation, which underpin cyclic energetic costs. These discrete seasonal life history events have consequences for conservation management (e.g., population viability) among wild fruit bat populations; however, little is known about the seasonality of reproduction in many pteropodid bat species. Here, we aimed to elucidate the reproductive biology of three species of pteropodid bats endemic to the island of Madagascar: Pteropus rufus, Eidolon dupreanum , and Rousettus madagascarensis. We leveraged plasma samples collected in part with a longitudinal field study, from 2019 and 2020. We adapted three standard reproductive assays previously validated in humans to quantify seasonal changes in reproductive hormones for bats and applied a mixture model approach to determine hormone cutoffs indicative of pregnancy in females and mating readiness in males. As predicted, we found that pregnant females showed the highest levels of estradiol and progesterone and adult males the highest levels of testosterone. Additionally, female P. rufus and R. madagascariensis showed clear seasonality in reproduction with peaks in estradiol and progesterone in August and October, respectively. Seasonality was less clearly discernible in female E. dupreanum and in male testosterone data. Our results demonstrate that hormone-based reproductive classification is a powerful tool for identifying reproductive status in free-ranging bats. These physiological data refine previously reported reproductive calendars critical for demographic modeling and conservation management of threatened Pteropodidae bats.

Introduction: Respiratory Syncytial Virus (RSV) is a primary source of acute lower respiratory tract infection (ALRTI), the leading cause of death in children under five. Over 99% of RSV-attributed deaths occur in low-income countries, including Madagascar. RSV transmission is linked to climate, driving highly seasonal dynamics. Methods: We used generalized additive models (GAMs) to identify correlates of reported RSV infections in Antananarivo, Madagascar from January 2011-December 2021, then fit catalytic models to cumulative age-structured incidence to estimate age-specific force of infection (FOI). We fit a time series Susceptible-Infected-Recovered (TSIR) model to the dataset to estimate weekly RSV transmission, then evaluated associations with precipitation, humidity, and temperature using generalized linear models. We used GAMs to quantify interannual trends in climate and assess whether significant deviations in RSV burden occurred in years representing climatic anomalies. Results: Reported RSV infections in Antananarivo were significantly associated with patient ages ≤2 years. Highest FOI was estimated in patients ≤1 year, with transmission declining to near-zero by age five before rising in older (60+) cohorts. TSIR models estimated a January–February peak in RSV transmission, which was strongly positively associated with precipitation and more weakly with temperature but negatively related to relative humidity. Precipitation, humidity, and temperature all increased across the study period in Antananarivo, while reported RSV infections remained stable. Significant deviations in RSV burden were not associated with clear climate anomalies. Conclusions: Stable rates of reported RSV infections in Antananarivo across the past decade may reflect contrasting impacts of elevated precipitation and increased humidity on transmission. If future climate changes yield more rapidly accelerating precipitation than humidity, this could accelerate RSV burden. Introduction of recently-developed public health interventions to combat RSV in low-income settings like Madagascar is essential to mitigating burden of disease (RSV), in particular any future climate-driven increases in transmission or severity. Key Messages: What is already known on this topic : RSV is an important driver of acute lower respiratory tract infections, which represent the leading cause of mortality in children under five across the globe. RSV demonstrates highly seasonal dynamics, as its transmission is linked to climate. What this study adds: We quantified correlates of RSV infection and estimated the seasonal transmission rate for RSV from reported patient data in Antananarivo, Madagascar. We found that RSV transmission is primarily concentrated in very young children (≤1 year) in Antananarivo and positively associated with high precipitation and low humidity, which focus most transmission in Madagascar’s January-February rainy season. How this study might affect research, practice, or policy: Our study suggests that RSV burden may intensify with future climate change, particularly higher rainfall. We emphasize the high public health importance of accelerating the introduction of recently-developed mAbs (Monoclonal Antibody) and vaccination interventions to combat RSV to low-income settings like Madagascar.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern—particularly Alpha, Beta, Delta, and Omicron—on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

SARS-CoV-2 across Africa: The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because of patchy data. Wilkinson et al . curated viral genomes collected in 2021 from several countries across the continent. Outbreaks during 2020 in each African country were initiated by imported cases, mostly from Europe. As the pandemic developed, case numbers in African countries were likely many times higher than reported, and subsequent waves of the pandemic appear to have been more severe. Consequently, high-transmission variants have emerged that have spread within the continent, and African countries must be included in global control efforts. —CA