Bats are the only flying mammals with more than 1,400 known species and are regarded as the second most diverse order of mammals after rodents. Bats harbor a wide range of viruses representing at least 28 viral families and are known reservoir hosts of multiple highly pathogenic viruses with pandemic threat.¹ These include henipaviruses (Nipah virus [NiV] and Hendra virus),^{2, 3 and 4} filoviruses (Ebola virus, Marburg virus, and Mengla virus),^{5, 6, 7, 8, 9, 10, 11, 12 and 13} and coronaviruses (severe acute respiratory syndrome coronavirus [SARS-CoV], SARS-CoV-2, and Middle East respiratory syndrome coronavirus [MERS-CoV]).^{14, 15, 16, 17, 18 and 19} For coronaviruses, more than 4,800 viral sequences have been detected in 543 bat species, highlighting the great diversity of bat coronaviruses. Among the four genera of coronaviruses, only alphacoronavirus and betacoronavirus were detected in bats in Asia, Europe, Africa, America, and Australasia. Of interest, only those from subgenera Sarbecovirus, Merbecovirus, Nobecovirus, and Hibecovirus have been detected in bats. Of the seven coronaviruses known to infect humans, bats are hosts of ancestral lineages for at least five of these coronaviruses.²⁰

In this chapter, we discuss what makes bats unique as reservoirs of highly pathogenic viruses, the diversity of the bat coronaviruses, key spillover event of bat coronaviruses, and how to assess the risk and mitigate the impact of future outbreak of bat coronaviruses.

Bats exhibit viral disease tolerance, described as the ability to sustain productive viral infection without notable disease symptoms or mortality.²¹ Significant evidence for this phenomenon comes from experimental infection studies in bats, particularly for zoonotic viruses that are highly pathogenic
upon spillover from the reservoir host species to humans and other animals. Marburg virus and NiV represent two clear examples of this phenomenon. Marburg virus was directly identified in Egyptian Rousettus bats (ERBs)²² and causes severe disease with a high case fatality rate in humans²³ and experimentally infected nonhuman primates.^{24, 25 and 26} In contrast, experimental infection of ERBs resulted in viral replication in blood and other tissues and seroconversion, without mortality or notable disease symptoms.^27,28 NiVs have been detected in bats of the Pteropus genus across multiple roost sites in South and Southeast Asia.^{29, 30, 31, 32 and 33} NiV infection causes viral encephalitis with a case fatality rate of 40% to 70% in humans^30,34,35 and causes severe disease and mortality in experimentally infected nonhuman primates.^36,37 Experimental infection of Pteropus bats resulted in seroconversion and intermittent virus shedding without any mortality, weight loss, or febrile responses observed.³⁸ Evidence for bats serving as a unique reservoir for coronaviruses, including the ancestral host for zoonotic coronaviruses SARS-CoV, SARS-CoV-2, and MERS-CoVs, comes from serologic, sequencing, and virus isolation data from a large number of studies in wild bats demonstrating natural infection or viral carriage. However, direct in vivo infection studies demonstrating asymptomatic infection of relevant cognate bat coronavirus species pairings, or the nature of the immune response mounted by bats to such infections, are still lacking. SARS-like sarbecoviruses are carried by insectivorous Rhinolophus bats, whereas MERS-like coronaviruses have been detected from the predominantly insectivorous Vespertilionidae and Nycteridae bat families,²⁰ which are harder to maintain in captivity compared to frugivorous bat species. Such studies also require isolation (or generation via recombinant technologies) of the ancestral coronavirus species related to the zoonotic coronavirus of interest. These pose significant scientific and procedural hurdles, which may be overcome in the future.

The evolution of flight is hypothesized to be linked to this unique viral reservoir status of bats. Powered flight imposes significant metabolic and physiologic demands on volant animals. The metabolic rate during flight is 3 to 5 times higher than the maximal metabolic rate observed during exercise in similar terrestrial mammals.^39,40 Consistent with this increased metabolic demand, bat genomes display positive selection of genes involved in oxidative phosphorylation in the mitochondria.⁴¹ High metabolic activity and increased functioning of the mitochondrial electron transport can lead to increased generation of free radicals and oxidative stress. Elevated body temperatures have been observed in bats, with temperatures reaching 40 °C to 42 °C during flight.^40,42 Prolonged flight and intense aerobic exercise can also lead to hypoxia within tissues. Various cellular receptors are capable of detecting endogenous danger signals released during metabolic stress or associated cell damage, including extracellular adenosine triphosphate (ATP) and mitochondrial DNA in the cytoplasm.^40,43,44 Similar markers of cellular damage are also produced during viral pathogenesis and can be sensed by the mammalian immune system to trigger an inflammatory response to fight infection. The hypothesis linking evolution of flight to viral reservoir status posits that bats evolved an altered immune response to avoid aberrant inflammatory activation from metabolic stresses associated with flight. This same mechanism led to the muted immune response and reduced immunopathology observed during viral infections in bats.

In support of this hypothesis, recent studies have uncovered numerous mechanisms for dampening the inflammatory responses in bats. This includes reduced induction of tumor necrosis factor (TNF)α cytokine observed upon stimulation of Eptesicus fuscus cells because of the presence of a c-rel binding motif in the TNF promoter region⁴⁵ and unique transcriptional expression of IDO1 in Eonycteris spelaea neutrophils. IDO1 encodes for indoleamine 2,3-dioxygenase, which mediates immunosuppression and immune tolerance by depleting tryptophan and producing kynurenine.⁴⁶ A notable and recurring theme is altered inflammasome-mediated signaling in bats. Inflammasomes are large multiprotein complexes that are activated through oligomerization triggered in response to a variety of “sterile” and pathogen-derived danger signals and that lead to the activation of inflammatory caspase-1, maturation and secretion of proinflammatory cytokines Interleukin-1 beta (IL-1β) and IL-18, and a lytic cell death termed pyroptosis.⁴⁷ All bat genomes sequenced to date lack the PYRIN and HIN domain (PYHIN) gene family, which includes the key intracellular DNA sensor AIM2 (absent in melanoma 2) which senses cytoplasmic DNA to trigger inflammasome assembly.⁴⁸ The stimulator of interferon genes (STING) receptor senses cytoplasmic DNA via cyclic GMP-AMP synthase (c-GAS)-mediated production of the secondary messenger cyclic guanosine monophosphate–adenosine monophosphate (c-GAMP). STING activation not only leads to upregulation of antiviral genes via the TBK1-IRF3 axis, but also plays a key role in activating the NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) inflammasome in myeloid cells via modulating cytoplasmic
potassium ion levels.⁴⁹ A key residue for phosphorylation and activation of STING, serine 358 which is conserved in other mammals, has been replaced by alternative amino acids in bat genomes, leading to dampened STING activation.⁵⁰ The NLRP3 inflammasome shows dampened activation in bat myeloid cells, including during in vitro viral infection, because of lower transcriptional priming and a novel splice variant and altered leucine-rich repeat domain that results in lowered activity compared to human or mouse homologs.⁵¹ The activity of bat caspase-1 and IL-1b cleavage site residues that determine cleavage efficiency has been reported to be reciprocally dampened in various bat species.⁵² Other additional mechanisms of inflammasome dampening are likely to emerge as research into bat immunology gains increasing attention. Overall, although the upstream evolutionary drivers for a dampened immune response in bats are still hypothetical, the impact of a plethora of dampening mechanisms on reduced immunopathology during viral infection seems clear.

An additional, perhaps complementary, explanation for the high viral diversity detected in Chiroptera is the remarkable adaptive radiation that ensued following the evolution of flight. Bats occupy a large diversity of ecologic niches and exhibit a range of dietary and physiologic adaptations.⁵³ The high species diversity of Chiroptera, second only to the order Rodentia, would positively impact the viral diversity hosted by this mammalian order. Taken together, a mounting body of scientific evidence—from both experimental studies on captive-bred or wild-caught bats, as well as metagenomic analysis of samples from wild bats—has contributed to our understanding of bats as a unique reservoir to a diverse group of viruses. Understanding the diversity of bat-borne viruses and studying the geographic, cultural, and ecologic drivers of viral spillover^54,55 are therefore important ongoing areas of research.

Nidovirales, a taxonomic order, comprises the families Coronaviridae, Arteriviridae, Roniviridae, Mesoniviridae, Medioniviridae, Abyssoviridae, Cremegaviridae, Gresnaviridae, Olifoviridae, Mononiviridae, Nanghoshaviridae, Nanhypoviridae, Euroniviridae, and Tobaniviridae (Figure 3.1) (https://ictv.global/report_9th/RNApos/Nidovirales/Coronaviridae). Coronaviridae are the largest family within the Nidovirales. Traditionally, coronaviruses are classified into three groups based on the antigenic relationships of the spike, membrane, and nucleocapsid proteins. Group 1 comprises of two human coronaviruses (229E and NL63) and three animal viruses (transmissible gastroenteritis virus [TGEV], canine coronavirus [CCoV], porcine epidemic diarrhea virus [PEDV]); group 2 comprises of human coronavirus OC43, HKU1, and SARS-CoV-1; and group 3 includes only avian viruses such as avian infectious bronchitis virus (IBV) (Table 3.1). More recently, there has been a reclassification based on the phylogenetic relationships. The newly established subfamily, Coronavirinae, now consists of four genera—Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus (Table 3.1). The alphacoronaviruses and betacoronaviruses infect only mammals and can cause respiratory illness in humans and gastroenteritis in animals. On the other hand, gammacoronaviruses and deltacoronaviruses are known to mainly infect birds, occasionally some can also infect mammals.

Coronaviruses were first isolated and identified as causative agents of animal disease in the 1930s when investigating animal diseases including infectious bronchitis in chickens, transmissible gastroenteritis in pigs, and severe hepatitis in mice. Over 90 years since the first discovery of the coronaviruses, only seven coronaviruses have been associated with human infection and diseases, and all originated from animals. Importantly, majority of them (SARS-CoV, SARS-CoV-2, MERS-CoV, HCoV-229E, and HCoV-NL63) are of bat origin, whereas two other human coronaviruses (HCoV-HKU-1 and HCoV-OC43) are likely of a murine origin. Furthermore, various evolution studies indicated that alphacoronavirus and betacoronavirus sourced their gene pool from bats, whereas deltacoronavirus and gammacoronavirus have genetic elements that originated from avian species.⁵⁶ In this section, we will focus our discussion on the known zoonotic coronaviruses of bat origin.