Bats are the only mammals capable of sustained flight and are notorious reservoir hosts for some of the world's most highly pathogenic viruses, including Nipah, Hendra, Ebola, and severe acute respiratory syndrome (SARS). To identify genetic changes associated with the development of bat-specific traits, we performed whole-genome sequencing and comparative analyses of two distantly related species, fruit bat Pteropus alecto and insectivorous bat Myotis davidii. We discovered an unexpected concentration of positively selected genes in the DNA damage checkpoint and nuclear factor κB pathways that may be related to the origin of flight, as well as expansion and contraction of important gene families. Comparison of bat genomes with other mammalian species has provided new insights into bat biology and evolution.

Viruses that originate in bats may be the most notorious emerging zoonoses that spill over from wildlife into domestic animals and humans. Understanding how these infections filter through ecological systems to cause disease in humans is of profound importance to public health. Transmission of viruses from bats to humans requires a hierarchy of enabling conditions that connect the distribution of reservoir hosts, viral infection within these hosts, and exposure and susceptibility of recipient hosts. For many emerging bat viruses, spillover also requires viral shedding from bats, and survival of the virus in the environment. Focusing on Hendra virus, but also addressing Nipah virus, Ebola virus, Marburg virus and coronaviruses, we delineate this cross-species spillover dynamic from the within-host processes that drive virus excretion to land-use changes that increase interaction among species. We describe how land-use changes may affect co-occurrence and contact between bats and recipient hosts. Two hypotheses may explain temporal and spatial pulses of virus shedding in bat populations: episodic shedding from persistently infected bats or transient epidemics that occur as virus is transmitted among bat populations. Management of livestock also may affect the probability of exposure and disease. Interventions to decrease the probability of virus spillover can be implemented at multiple levels from targeting the reservoir host to managing recipient host exposure and susceptibility.

The genus Henipavirus in the family Paramyxoviridae contains two viruses, Hendra virus (HeV) and Nipah virus (NiV) for which pteropid bats act as the main natural reservoir. Each virus also causes serious and commonly lethal infection of people as well as various species of domestic animals, however little is known about the associated mechanisms of pathogenesis. Here, we report the isolation and characterization of a new paramyxovirus from pteropid bats, Cedar virus (CedPV), which shares significant features with the known henipaviruses. The genome size (18,162 nt) and organization of CedPV is very similar to that of HeV and NiV; its nucleocapsid protein displays antigenic cross-reactivity with henipaviruses; and it uses the same receptor molecule (ephrin- B2) for entry during infection. Preliminary challenge studies with CedPV in ferrets and guinea pigs, both susceptible to infection and disease with known henipaviruses, confirmed virus replication and production of neutralizing antibodies although clinical disease was not observed. In this context, it is interesting to note that the major genetic difference between CedPV and HeV or NiV lies within the coding strategy of the P gene, which is known to play an important role in evading the host innate immune system. Unlike HeV, NiV, and almost all known paramyxoviruses, the CedPV P gene lacks both RNA editing and also the coding capacity for the highly conserved V protein. Preliminary study indicated that CedPV infection of human cells induces a more robust IFN-β response than HeV.

The influenza A virus genome is composed of eight negativesense RNA segments (22, 26), which can encode up to 11 viral proteins (3, 23). Upon infection, the viral RNA (vRNA) is transported to the nucleus, the site of vRNA transcription and replication. At late stages of the infectious cycle, the viral ribonucleoprotein complex, composed of the three influenza polymerase proteins, the nucleoprotein, and vRNA, is exported from the nucleus in association with the influenza virus matrix (M1) and nuclear export (NEP) proteins (5). The final step of the virus replication cycle involves the assembly of the viral structural proteins and the packaging of the viral genome. For a virus particle to be fully infectious, it must contain a full complement of the eight vRNA segments. The process by which this packaging occurs is not well understood. However, it is known that vRNA is specifically packaged in preference to cellular RNAs and that the different vRNAs are present in an equimolar ratio within a population of virus particles (21).Two models have been proposed for the packaging of vRNA into budding virions: the random incorporation model and the selective incorporation model (23). The random incorporation model assumes that a common structural feature is present on all vRNAs which enables them to be randomly incorporated into budding virions. In other words, the virus randomly incorporates vRNA into budding virions and does not differentiate among the different segments (4). This means that the likelihood of a virion obtaining a full complement of the eight vRNAs is determined entirely by chance. This model is supported by evidence that infectious viruses may possess more than eight vRNAs (8). Mathematical modeling suggests that if eight vRNAs are packaged randomly, 0.24% of released virus particles would contain a full complement of vRNAs and be infectious (1,8). If 12 vRNAs were packaged randomly, the mathematical models suggest that infectivity increases to approximately 10%, which is comparable with the experimental data (6). As only 1 to 2% of the weight of the influenza virus particle is vRNA, it is difficult to accurately quantify the exact number of vRNA segments packaged. The earliest evidence suggesting that influenza vRNAs have packaging signals was from Luytjes et al. (14). Utilizing both the 3Ј and 5Ј terminal untranslated regions of the NS gene, it was possible to package a chloramphenicol acetyltransferase gene into influenza virus particles. This foreign gene was packaged into infectious particles and passaged several times, suggesting that the terminal 22 5Ј and 26 3Ј nucleotides are sufficient to provide the signals for RNA transcription and replication as well as for the packaging of RNA into influenza virus particles.The selective incorporation model suggests that each vRNA segment contains a unique "packaging signal" allowing it to act independently, with each vRNA segment being packaged selectively. Evidence supporting this model comes from several reports demonstrating that defective interfering ...

The genome of the influenza A virus is composed of eight different segments of negative-sense RNA. These eight segments are incorporated into budding virions in an equimolar ratio through a mechanism that is not fully understood. Two different models have been proposed for packaging the viral ribonucleoproteins into newly assembling virus particles: the random-incorporation model and the selective-incorporation model. In the last few years, increasing evidence from many different laboratories that supports the selective-incorporation model has been accumulated. In particular, different groups have shown that some large viral RNA regions within the coding sequences at both the 5 and 3 ends of almost every segment are sufficient for packaging foreign RNA sequences. If the packaging regions are crucial for the viability of the virus, we would expect them to be conserved. Using large-scale analysis of influenza A virus sequences, we developed a method of identifying conserved RNA regions whose conservation cannot be explained by population structure or amino acid conservation. Interestingly, the conserved sequences are located within the regions identified as important for efficient packaging. By utilizing influenza virus reverse genetics, we have rescued mutant viruses containing synonymous mutations within these highly conserved regions. Packaging of viral RNAs in these viruses was analyzed by reverse transcription using a universal primer and quantitative PCR for individual segments. Employing this approach, we have identified regions in the polymerase gene segments that, if mutated, result in reductions of more than 90% in the packaging of that particular polymerase viral RNA. Reductions in the level of packaging of a polymerase viral RNA frequently resulted in reductions of other viral RNAs as well, and the results form a pattern of hierarchy of segment interactions. This work provides further evidence for a selective packaging mechanism for influenza A viruses, demonstrating that these highly conserved regions are important for efficient packaging.The influenza A virus genome consists of eight negativesense RNA segments (19, 24), encoding up to 11 viral proteins (2,20). During the infection of target cells, influenza viral RNA (vRNA) replication and transcription occurs in the nucleus. In order to be packaged into progeny virions, the vRNA is transported from the nucleus as a ribonucleoprotein complex composed of the three influenza virus polymerase proteins, the nucleoprotein (NP), and the vRNA, in association with the influenza virus matrix 1 (M1) protein and nuclear export protein (3). The process by which the vRNA is packaged is not well understood. However, it is known that vRNA is specifically packaged in preference to other cellular RNAs and that the different vRNAs are present in an equimolar ratio within a population of virus particles (18). For a virus particle to be fully infectious, it must contain a full complement of the eight vRNA segments.Two simple models have been hypothesized for the packagi...

In recent years, the emergence of several highly pathogenic zoonotic diseases in humans has led to a renewed emphasis on the interconnectedness of human, animal, and environmental health, otherwise known as One Health. For example, Hendra virus (HeV), a zoonotic paramyxovirus, was discovered in 1994, and since then, infections have occurred in 7 humans, each of whom had a strong epidemiologic link to similarly affected horses. As a consequence of these outbreaks, eradication of bat populations was discussed, despite their crucial environmental roles in pollination and reduction of the insect population. We describe the development and evaluation of a vaccine for horses with the potential for breaking the chain of HeV transmission from bats to horses to humans, thereby protecting horse, human, and environmental health. The HeV vaccine for horses is a key example of a One Health approach to the control of human disease.

BackgroundBats are the suspected natural reservoir hosts for a number of new and emerging zoonotic viruses including Nipah virus, Hendra virus, severe acute respiratory syndrome coronavirus and Ebola virus. Since the discovery of SARS-like coronaviruses in Chinese horseshoe bats, attempts to isolate a SL-CoV from bats have failed and attempts to isolate other bat-borne viruses in various mammalian cell lines have been similarly unsuccessful. New stable bat cell lines are needed to help with these investigations and as tools to assist in the study of bat immunology and virus-host interactions.Methodology/FindingsBlack flying foxes (Pteropus alecto) were captured from the wild and transported live to the laboratory for primary cell culture preparation using a variety of different methods and culture media. Primary cells were successfully cultured from 20 different organs. Cell immortalisation can occur spontaneously, however we used a retroviral system to immortalise cells via the transfer and stable production of the Simian virus 40 Large T antigen and the human telomerase reverse transcriptase protein. Initial infection experiments with both cloned and uncloned cell lines using Hendra and Nipah viruses demonstrated varying degrees of infection efficiency between the different cell lines, although it was possible to infect cells in all tissue types.Conclusions/SignificanceThe approaches developed and optimised in this study should be applicable to bats of other species. We are in the process of generating further cell lines from a number of different bat species using the methodology established in this study.

During 2014, henipavirus infection caused severe illness among humans and horses in southern Philippines; fatality rates among humans were high. Horse-to-human and human-to-human transmission occurred. The most likely source of horse infection was fruit bats. Ongoing surveillance is needed for rapid diagnosis, risk factor investigation, control measure implementation, and further virus characterization.