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

HAdV-B7 might be reemerging in the United States.

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Background In the United States, the seasonality of respiratory syncytial virus (RSV) has traditionally been defined on the basis of weeks during which antigen-based tests detect RSV in >10% of specimens (hereafter, the “10% threshold”). Because molecular testing has become more widely used, we explored the extent of polymerase chain reaction (PCR)–based RSV testing and its impact on determining the seasonality of RSV. Methods We assessed antigen- and PCR-based RSV reports submitted to the National Respiratory and Enteric Virus Surveillance System during July 2005–June 2015. To characterize RSV seasons by using PCR-based reports, we assessed the traditional 10% threshold; subsequently, we developed 3 methods based on either PCR-based detections or the percentage of positive test results. Results The annual number of PCR-based reports increased 200-fold during 2005–2015, while the annual number of antigen-based reports declined. The weekly percentage of specimens positive for RSV by PCR was less than that for antigen-detection tests; accordingly, the 10% threshold excluded detections by PCR and so was imprecise for characterizing RSV seasons. Among our PCR-specific approaches, the most sensitive and consistent method captured 96%–98% of annual detections within a season, compared with 82%–94% captured using the traditional method. Conclusions PCR-based reports are increasingly relevant for RSV surveillance and determining the seasonality of RSV. These PCR-specific methods provide a more comprehensive understanding of RSV trends, particularly in settings where testing and reporting are most active. Diagnostic practices will vary by locality and should be understood before choosing which method to apply.

Middle East respiratory syndrome (MERS) cases continue to be reported from the Middle East. Evaluation and testing of patients under investigation (PUIs) for MERS are recommended. In 2013–2014, two imported cases were detected among 490 US PUIs. Continued awareness is needed for early case detection and implementation of infection control measures.