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Abstract Bats (order: Chiroptera) are known to host a diverse range of viruses, some of which present a human 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.

Introduction Respiratory syncytial virus (RSV) is a primary source of acute lower respiratory tract infection, the leading cause of death in children under 5. 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 generalised additive models (GAMs) to identify correlates of reported RSV infections in Antananarivo, Madagascar, from January 2011 to 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 generalised 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 patients aged ≤2 years. Highest FOI was estimated in patients aged ≤1 year, with transmission declining to near-zero by age 5 before rising in older (60+) cohorts. TSIR models estimated a January to 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 disease burden, in particular to combat any future climate-driven increases in transmission or severity.