For RNA viruses, rapid viral evolution and the biological similarity of closely related host species have been proposed as key determinants of the occurrence and long-term outcome of cross-species transmission. Using a data set of hundreds of rabies viruses sampled from 23 North American bat species, we present a general framework to quantify per capita rates of cross-species transmission and reconstruct historical patterns of viral establishment in new host species using molecular sequence data. These estimates demonstrate diminishing frequencies of both cross-species transmission and host shifts with increasing phylogenetic distance between bat species. Evolutionary constraints on viral host range indicate that host species barriers may trump the intrinsic mutability of RNA viruses in determining the fate of emerging host-virus interactions.

Two Nipah virus encephalitis outbreaks in Bangladesh may be associated with person-to-person transmission.

Bats harbor a large diversity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat samples collected in Kenya from 2007 to 2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating in Triaenops bats and 229E-like viruses circulating in Hipposideros bats, with the breakpoint located near 5= and 3= ends of the spike (S) protein gene. In addition, two further interspecies recombination events involving the S gene were identified, suggesting that this region may represent a recombination "hot spot" in CoV genomes. Finally, using a combination of phylogenetic and distance-based approaches, we showed that the genetic diversity of bat CoVs is primarily structured by host species and subsequently by geographic distances.IMPORTANCE Understanding the driving forces of cross-species virus transmission is central to understanding the nature of disease emergence. Previous studies have demonstrated that bats are the ultimate reservoir hosts for a number of coronaviruses (CoVs), including ancestors of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and human CoV 229E (HCoV-229E). However, the evolutionary pathways of bat CoVs remain elusive. We provide evidence for natural recombination between distantly related African bat coronaviruses associated with Triaenops afer and Hipposideros sp. bats that resulted in a NL63-like virus, an ancestor of the human pathogen HCoV-NL63. These results suggest that interspecies recombination may play an important role in CoV evolution and the emergence of novel CoVs with zoonotic potential.KEYWORDS Africa, bats, coronavirus, HCoV-229E, HCoV-NL63, recombination, zoonoses C oronaviruses (CoVs) (subfamily Coronavirinae, family Coronaviridae, order Nidovirales) are common infectious agents that infect a wide range of hosts, including humans, causing respiratory, gastrointestinal, liver, and neurologic diseases, and that possess the largest genomes of any RNA viruses described to date (1). The subfamily Coronavirinae is currently classified into four genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus (2). The alphacoronaviruses (alpha-CoVs) and

Although there are over 1,150 bat species worldwide, the diversity of viruses harbored by bats has only recently come into focus as a result of expanded wildlife surveillance. Such surveys are of importance in determining the potential for novel viruses to emerge in humans, and for optimal management of bats and their habitats. To enhance our knowledge of the viral diversity present in bats, we initially surveyed 415 sera from African and Central American bats. Unbiased high-throughput sequencing revealed the presence of a highly diverse group of bat-derived viruses related to hepaciviruses and pegiviruses within the family Flaviridae. Subsequent PCR screening of 1,258 bat specimens collected worldwide indicated the presence of these viruses also in North America and Asia. A total of 83 bat-derived viruses were identified, representing an infection rate of nearly 5%. Evolutionary analyses revealed that all known hepaciviruses and pegiviruses, including those previously documented in humans and other primates, fall within the phylogenetic diversity of the bat-derived viruses described here. The prevalence, unprecedented viral biodiversity, phylogenetic divergence, and worldwide distribution of the bat-derived viruses suggest that bats are a major and ancient natural reservoir for both hepaciviruses and pegiviruses and provide insights into the evolutionary history of hepatitis C virus and the human GB viruses.

Diverse coronaviruses have been identifi ed in bats from several continents but not from Africa. We identifi ed group 1 and 2 coronaviruses in bats in Kenya, including SARS-related coronaviruses. The sequence diversity suggests that bats are well-established reservoirs for and likely sources of coronaviruses for many species, including humans.T he 2003 outbreak of severe acute respiratory syndrome (SARS) generated renewed interest in coronaviruses (CoV) and the source for the SARS CoV that caused the outbreak in humans (1). Serologic studies demonstrated that the virus had not previously circulated in human populations to any large extent and suggested a source of zoonotic origin (2-4). A likely natural viral reservoir for the virus was not identifi ed until horseshoe bats (Rhinolophus spp.) in several regions in the People's Republic of China were demonstrated to harbor SARS-like CoVs (5). Subsequently, a number of other SARS-like CoVs, as well as CoVs from antigenic groups I and II, were identifi ed from bats in Asia, Europe, and North America, and coronavirus antibodies were detected in African bat species (6-11). It is not surprising that a growing number of CoVs have been detected in bats. To date, >60 viral species have been detected in bats because their biodiversity (second only to rodents), high population densities, wide distribution, and ability to fl y over long distances allow them to harbor and easily spread multiple infectious agents. Bats have long been known as natural hosts for lyssaviruses and more recently have been recognized as potential reservoirs for emerging human pathogens, including Ebola, Marburg, Nipah, and Hendra viruses in addition to SARS-CoV (12,13). The StudyGiven the association of bats with emerging infectious diseases, fi eld surveys were performed during July-August 2006 in the southern portion of Kenya (Figure 1). The selection of sites was based on preliminary data regarding bat roost locations and observations of bats in the fi eld during the survey. Attempts were made to collect specimens from 10-20 animals of each species present in each location. Bats were captured manually and by using mist nets and hand nets; adults and subadults of both sexes were captured. Each bat was measured, sexed, and identifi ed to the genus or species level when possible. Blood samples and oral and fecal swabs were collected; the animals were then euthanized in compliance with fi eld protocol. Blood, fecal swabs, and selected tissue samples were transported on dry ice from the fi eld and stored at -80°C.Fecal swabs (n = 221; Table) were screened for the presence of CoV RNA using 2 semi-nested reverse transcription-PCR (RT-PCR) assays. For the pan-coronavirus RT-PCR, conserved primers were designed from highly conserved regions of the RNA-dependent RNA polymerase (RdRp) gene 1b based on available CoV sequences (1st and 2nd round forward 5′-ATGGGITGGGAY TATCCWAARTGTG-3′; 1st round reverse 5′-AATTAT ARCAIACAACISYRTCRTCA-3′; 2nd round reverse 5′-CTAGTICCACCIGGYTTWANRTA-3′). For the pan-bat

In nature, rabies virus (RABV; genus Lyssavirus, family Rhabdoviridae) represents an assemblage of phylogenetic lineages, associated with specific mammalian host species. Although it is generally accepted that RABV evolved originally in bats and further shifted to carnivores, mechanisms of such host shifts are poorly understood, and examples are rarely present in surveillance data. Outbreaks in carnivores caused by a RABV variant, associated with big brown bats, occurred repeatedly during 2001–2009 in the Flagstaff area of Arizona. After each outbreak, extensive control campaigns were undertaken, with no reports of further rabies cases in carnivores for the next several years. However, questions remained whether all outbreaks were caused by a single introduction and further perpetuation of bat RABV in carnivore populations, or each outbreak was caused by an independent introduction of a bat virus. Another question of concern was related to adaptive changes in the RABV genome associated with host shifts. To address these questions, we sequenced and analyzed 66 complete and 20 nearly complete RABV genomes, including those from the Flagstaff area and other similar outbreaks in carnivores, caused by bat RABVs, and representatives of the major RABV lineages circulating in North America and worldwide. Phylogenetic analysis demonstrated that each Flagstaff outbreak was caused by an independent introduction of bat RABV into populations of carnivores. Positive selection analysis confirmed the absence of post-shift changes in RABV genes. In contrast, convergent evolution analysis demonstrated several amino acids in the N, P, G and L proteins, which might be significant for pre-adaptation of bat viruses to cause effective infection in carnivores. The substitution S/T242 in the viral glycoprotein is of particular merit, as a similar substitution was suggested for pathogenicity of Nishigahara RABV strain. Roles of the amino acid changes, detected in our study, require additional investigations, using reverse genetics and other approaches.

In February 2019, following the annual taxon ratification vote, the order Mononegavirales was amended by the addition of four new subfamilies and 12 new genera and the creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

During lyssavirus surveillance, 1,221 bats of at least 30 species were collected from 25 locations in Kenya. One isolate of Lagos bat virus (LBV) was obtained from a dead Eidolon helvum fruit bat. The virus was most similar phylogenetically to LBV isolates from Senegal (1985) and from France (imported from Togo or Egypt; 1999), sharing with these viruses 100% nucleoprotein identity and 99.8 to 100% glycoprotein identity. This genome conservancy across space and time suggests that LBV is well adapted to its natural host species and that populations of reservoir hosts in eastern and western Africa have sufficient interactions to share pathogens. High virus concentrations, in addition to being detected in the brain, were detected in the salivary glands and tongue and in an oral swab, suggesting that LBV is transmitted in the saliva. In other extraneural organs, the virus was generally associated with innervations and ganglia. The presence of infectious virus in the reproductive tract and in a vaginal swab implies an alternative opportunity for transmission. The isolate was pathogenic for laboratory mice by the intracerebral and intramuscular routes. Serologic screening demonstrated the presence of LBV-neutralizing antibodies in E. helvum and Rousettus aegyptiacus fruit bats. In different colonies the seroprevalence ranged from 40 to 67% and 29 to 46% for E. helvum and R. aegyptiacus, respectively. Nested reverse transcription-PCR did not reveal the presence of viral RNA in oral swabs of bats in the absence of brain infection. Several large bat roosts were identified in areas of dense human populations, raising public health concerns for the potential of lyssavirus infection.