Bat Genomes: Bats are of great interest because of their ability to fly and as hosts for infectious disease. Zhang et al. (p. 456 , published online 20 December) sequenced the genomes of two distantly related bat species, David's Myotis and Black flying fox. Analysis of the two genomes revealed likely changes that accompanied the evolution of bats, including selection for increased expression of genes involved in the oxidative phosphorylation pathway needed to generate the energy required for flight. Furthermore, while some immune genes have been lost, others are under positive selection, which may potentially explain bats' status as viral reservoirs.

Significance: Here we provide what is, to our knowledge, the first gene map of the type I IFN region of any bat species with the sequence of the type I IFN locus of the Australian black flying fox,Pteropus alecto.The bat IFN locus contains fewer IFN genes compared with any other mammal sequenced to date, including only threeIFN-αgenes. We also demonstrate that batIFN-αgenes are constitutively expressed in unstimulated bat tissues and cells and that their expression is unaffected by viral infection. This unusual pattern ofIFN-αexpression has not been described in any other species to our knowledge and has important implications for the role of innate immunity in the ability of bats to coexist with viruses in the absence of disease.

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.

Bats are reservoir hosts of many important viruses that cause substantial disease in humans, including coronaviruses, filoviruses, lyssaviruses and henipaviruses. The viruses do not appear to cause disease in the reservoir bats, thus an explanation for the dichotomous outcomes of infections of humans and bat reservoirs remains to be determined. Bats appear to have a few unusual features that may account for these differences, including evidence of constitutive interferon (IFN) activation and greater combinatorial diversity in immunoglobulin genes that do not undergo substantial affinity maturation. We propose these features may, in part, account for why bats can host these viruses without disease, and how they may contribute to the highly pathogenic nature of bat-borne viruses after spillover into humans. Because of the constitutive IFN activity, bat-borne viruses may be shed at low levels from bat cells. With large naïve antibody repertoires, bats may control the limited virus replication without the need for rapid affinity maturation, and this may explain why bats typically have low antibody titers to viruses. However, because bat viruses have evolved in high IFN environments, they have enhanced countermeasures against the IFN response. Thus, upon infection of human cells, where the IFN response is not constitutive, the viruses overwhelm the IFN response, leading to abundant virus replication and pathology.