A review of mechanistic models of viral dynamics in bat reservoirs for zoonotic disease

Characterization of Ravn virus viral shedding dynamics in experimentally infected Egyptian rousette bats (Rousettus aegypticus)

Marburg virus (MARV) and Ravn virus (RAVV), the only two known members of the species Orthomarburgvirus marburgense (family Filoviridae), are causative agents of Marburg virus disease, a severe viral disease that typically emerges in sub-Saharan Africa and is characterized by human-to-human transmission and high case fatalities. Despite the robust characterization of MARV experimental infection in Egyptian rousette bats (ERBs; Rousettus aegyptiacus; common name: Egyptian rousettes), a natural MARV reservoir, experimental infection with RAVV in ERBs has not been completed. Here, we experimentally infect 12 ERBs with RAVV and quantify viral loads in blood, oral swabs, and rectal swabs over a 21-day timeline with serological and cumulative shedding data and baseline clinical parameters. Compared to previously described experimental MARV infection in ERBs, these bats experimentally inoculated with RAVV had significantly higher and prolonged rectal viral shedding loads, as well as significantly prolonged oral shedding and higher peak viremia. All ERBs seroconverted by 21 days post-infection. Additionally, all ERBs demonstrated marked heterogeneity in RAVV viral shedding loads consistent with the Pareto Principle and viral "supershedders." Our results introduce the possibility of variation in transmission dynamics and subsequent spillover differences between RAVV and MARV.IMPORTANCERavn virus, along with Marburg virus, causes severe viral disease in humans with high fatality but little to no clinical disease in its reservoir host, the Egyptian rousette bat. Our findings provide important insights into how Ravn virus behaves in its natural reservoir host, showing that Ravn virus infection followed a similar timeline to Marburg virus infection, with virus detected in blood, saliva, and feces. However, Ravn virus-infected bats had higher levels of viral shedding and shed the virus for a longer period, particularly in feces, compared to Marburg virus. These differences in viral shedding may impact the spread of the virus within bat populations and potentially alter the likelihood of spillover into humans, non-human primates, and other animal species. These insights are crucial for understanding Ravn virus maintenance in its bat reservoir and improving our ability to mitigate or prevent future human outbreaks.

Advances in understanding bat infection dynamics across biological scales

Over the past two decades, research on bat-associated microbes such as viruses, bacteria and fungi has dramatically increased. Here, we synthesize themes from a conference symposium focused on advances in the research of bats and their microbes, including physiological, immunological, ecological and epidemiological research that has improved our understanding of bat infection dynamics at multiple biological scales. We first present metrics for measuring individual bat responses to infection and challenges associated with using these metrics. We next discuss infection dynamics within bat populations of the same species, before introducing complexities that arise in multi-species communities of bats, humans and/or livestock. Finally, we outline critical gaps and opportunities for future interdisciplinary work on topics involving bats and their microbes.

Applications of VirScan to broad serological profiling of bat reservoirs for emerging zoonoses

Introduction

Bats are important providers of ecosystem services such as pollination, seed dispersal, and insect control but also act as natural reservoirs for virulent zoonotic viruses. Bats host multiple viruses that cause life-threatening pathology in other animals and humans but, themselves, experience limited pathological disease from infection. Despite bats' importance as reservoirs for several zoonotic viruses, we know little about the broader viral diversity that they host. Bat virus surveillance efforts are challenged by difficulties of field capture and the limited scope of targeted PCR- or ELISA-based molecular and serological detection. Additionally, virus shedding is often transient, thus also limiting insights gained from nucleic acid testing of field specimens. Phage ImmunoPrecipitation Sequencing (PhIP-Seq), a broad serological tool used previously to comprehensively profile viral exposure history in humans, offers an exciting prospect for viral surveillance efforts in wildlife, including bats.

Methods

Here, for the first time, we apply PhIP-Seq technology to bat serum, using a viral peptide library originally designed to simultaneously assay exposures to the entire human virome.

Results

Using VirScan, we identified past exposures to 57 viral genera-including betacoronaviruses, henipaviruses, lyssaviruses, and filoviruses-in semi-captive Pteropus alecto and to nine viral genera in captive Eonycteris spelaea. Consistent with results from humans, we find that both total peptide hits (the number of enriched viral peptides in our library) and the corresponding number of inferred past virus exposures in bat hosts were correlated with poor bat body condition scores and increased with age. High and low body condition scores were associated with either seropositive or seronegative status for different viruses, though in general, virus-specific age-seroprevalence curves defied assumptions of lifelong immunizing infection, suggesting that many bat viruses may circulate via complex transmission dynamics.

Discussion

Overall, our work emphasizes the utility of applying biomedical tools, like PhIP-Seq, first developed for humans to viral surveillance efforts in wildlife, while highlighting opportunities for taxon-specific improvements.

Detection and genetic characterization of circoviruses in more than 80 bat species from eight countries on four continents

Several bat-associated circoviruses and circular rep-encoding single-stranded DNA (CRESS DNA) viruses have been described, but the exact diversity and host species of these viruses are often unknown. Our goal was to describe the diversity of bat-associated circoviruses and cirliviruses, thus, 424 bat samples from more than 80 species were collected on four continents. The samples were screened for circoviruses using PCR and the resulting amino acid sequences were subjected to phylogenetic analysis. The majority of bat strains were classified in the genus Circovirus and some strains in the genus Cyclovirus and the clades CRESS1 and CRESS3. Some strains, however, could only be classified at the taxonomic level of the order and were not classified in any of the accepted or proposed clades. In the family Circoviridae, 71 new species have been predicted. This screening of bat samples revealed a great diversity of circoviruses and cirliviruses. These studies underline the importance of the discovery and description of new cirliviruses and the need to establish new species and families in the order Cirlivirales.

Quantifying Spillover Risk with an Integrated Bat-Rabies Dynamic Modeling Framework

Vampire bat-transmitted rabies has recently become the leading cause of rabies mortality in both humans and livestock in Latin America. Evaluating risk of transmission from bats to other animal species has thus become a priority in the region. An integrated bat-rabies dynamic modeling framework quantifying spillover risk to cattle farms was developed. The model is spatially explicit and is calibrated to the state of São Paulo, using real roost and farm locations. Roost and farm characteristics, as well as environmental data through an ecological niche model, are used to modulate rabies transmission. Interventions aimed at reducing risk in roosts (such as bat culling or vaccination) and in farms (cattle vaccination) were considered as control strategies. Both interventions significantly reduce the number of outbreaks in farms and disease spread (based on distance from source), with control in roosts being a significantly better intervention. High-risk areas were also identified, which can support ongoing programs, leading to more effective control interventions.

Transmission dynamics of lyssavirus in Myotis myotis: mechanistic modelling study based on longitudinal seroprevalence data

We investigated the transmission dynamics of lyssavirus in Myotis myotis and Myotis blythii, using serological, virological, demographic and ecological data collected between 2015 and 2022 from two maternity colonies in northern Italian churches. Despite no lyssavirus detection in 556 bats sampled over 11 events by reverse transcription-polymerase chain reaction (RT-PCR), 36.3% of 837 bats sampled over 27 events showed neutralizing antibodies to European bat lyssavirus 1, with a significant increase in summers. By fitting sets of mechanistic models to seroprevalence data, we investigated factors that influenced lyssavirus transmission within and between years. Five models were selected as a group of final models: in one model, a proportion of exposed bats (median model estimate: 5.8%) became infectious and died while the other exposed bats recovered with immunity without becoming infectious; in the other four models, all exposed bats became infectious and recovered with immunity. The final models supported that the two colonies experienced seasonal outbreaks driven by: (i) immunity loss particularly during hibernation, (ii) density-dependent transmission, and (iii) a high transmission rate after synchronous birthing. These findings highlight the importance of understanding ecological factors, including colony size and synchronous birthing timing, and potential infection heterogeneities to enable more robust assessments of lyssavirus spillover risk.

Genomic representation predicts an asymptotic host adaptation of bat coronaviruses using deep learning

Introduction

Coronaviruses (CoVs) are naturally found in bats and can occasionally cause infection and transmission in humans and other mammals. Our study aimed to build a deep learning (DL) method to predict the adaptation of bat CoVs to other mammals.

Methods

The CoV genome was represented with a method of dinucleotide composition representation (DCR) for the two main viral genes, ORF1ab and Spike. DCR features were first analyzed for their distribution among adaptive hosts and then trained with a DL classifier of convolutional neural networks (CNN) to predict the adaptation of bat CoVs.

Results and discussion

The results demonstrated inter-host separation and intra-host clustering of DCR-represented CoVs for six host types: Artiodactyla, Carnivora, Chiroptera, Primates, Rodentia/Lagomorpha, and Suiformes. The DCR-based CNN with five host labels (without Chiroptera) predicted a dominant adaptation of bat CoVs to Artiodactyla hosts, then to Carnivora and Rodentia/Lagomorpha mammals, and later to primates. Moreover, a linear asymptotic adaptation of all CoVs (except Suiformes) from Artiodactyla to Carnivora and Rodentia/Lagomorpha and then to Primates indicates an asymptotic bats-other mammals-human adaptation.

Conclusion

Genomic dinucleotides represented as DCR indicate a host-specific separation, and clustering predicts a linear asymptotic adaptation shift of bat CoVs from other mammals to humans via deep learning.

Gut microbiota of bats: pro-mutagenic properties and possible frontiers in preventing emerging disease

Bats are potential natural reservoirs for emerging viruses, causing deadly human diseases, such as COVID-19, MERS, SARS, Nipah, Hendra, and Ebola infections. The fundamental mechanisms by which bats are considered “living bioreactors” for emerging viruses are not fully understood. Some studies suggest that tolerance to viruses is linked to suppressing antiviral immune and inflammatory responses due to DNA damage by energy generated to fly. Our study reveals that bats' gut bacteria could also be involved in the host and its microbiota's DNA damage. We performed screening of lactic acid bacteria and bacilli isolated from bats' feces for mutagenic and oxidative activity by lux-biosensors. The pro-mutagenic activity was determined when expression of recA increased with the appearance of double-strand breaks in the cell DNA, while an increase of katG expression in the presence of hydroxyl radicals indicated antioxidant activity. We identified that most of the isolated bacteria have pro-mutagenic and antioxidant properties at the same time. This study reveals new insights into bat gut microbiota's potential involvement in antiviral response and opens new frontiers in preventing emerging diseases originating from bats.

Comparative Computational Modeling of the Bat and Human Immune Response to Viral Infection with the Comparative Biology Immune Agent Based Model

Given the impact of pandemics due to viruses of bat origin, there is increasing interest in comparative investigation into the differences between bat and human immune responses. The practice of comparative biology can be enhanced by computational methods used for dynamic knowledge representation to visualize and interrogate the putative differences between the two systems. We present an agent based model that encompasses and bridges differences between bat and human responses to viral infection: the comparative biology immune agent based model, or CBIABM. The CBIABM examines differences in innate immune mechanisms between bats and humans, specifically regarding inflammasome activity and type 1 interferon dynamics, in terms of tolerance to viral infection. Simulation experiments with the CBIABM demonstrate the efficacy of bat-related features in conferring viral tolerance and also suggest a crucial role for endothelial inflammasome activity as a mechanism for bat systemic viral tolerance and affecting the severity of disease in human viral infections. We hope that this initial study will inspire additional comparative modeling projects to link, compare, and contrast immunological functions shared across different species, and in so doing, provide insight and aid in preparation for future viral pandemics of zoonotic origin.

Update on the Phylodynamics of SADS-CoV

Coronaviruses are known to be harmful and heterogeneous viruses, able to infect a large number of hosts. Among them, SADS-CoV (Swine Acute Diarrhea Syndrome Coronavirus), also known as PEAV (Porcine Enteric Alphacoronavirus), or SeA-CoV (Swine Enteric Alphacoronavirus), is the most recent Alphacoronavirus discovered, and caused several outbreaks reported in Chinese swine herds between late 2016 and 2019. We performed an upgraded phylodinamic reconstruction of SADS-CoV based on all whole genomes available on 21 June 2021. Results showed a very close relationship between SADS-CoV and HKU2-like CoV, which may represent the evolutionary intermediate step towards the present SADS-CoV. The direct progenitor of SADS-CoV is so far unknown and, although it is well known that horseshoe bats are reservoirs for Rhinolophus bat coronavirus HKU2-like (HKU2-like CoVs), the transmission path from bats to pigs is still unclear. The discrepancies in the phylogenetic position of rodent CoV, when different molecular markers were considered, corroborate the recombination hypothesis, suggesting that wild rats, which are frequent in farms, may have played a key role. The failure of the attempt at molecular dating, due to the lack of a clock signal, also corroborates the occurrence of a recombination event hypothesis. Zoonotic infections originating in wildlife can easily become a significant threat for human health. In such a context, due to the high recombination and cross-species capabilities of Coronavirus, SADS-CoV represents a possible high-risk pathogen for humans which needs a constant molecular monitoring.

The Worldwide Effort to Develop Vaccines for COVID-19

There have been recent encouraging reports about the development of vaccines for COVID-19. Given the scale and effects of this pandemic on public health and economies worldwide, there has been an unprecedented approach across the globe, leading to the emergence of vaccine candidates many times faster than the normal process would allow. This review gives up-to-date information as of November 28, 2020, on the latest developments in this area and covers the plans to roll out the most promising vaccines across the entire world to halt the spread of this devastating virus.