Alphacoronaviruses in New World Bats: Prevalence, Persistence, Phylogeny, and Potential for Interaction with Humans

Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted

Post-glacial colonisation of Europe by the wood mouse, Apodemus sylvaticus : evidence of a northern refugium and dispersal with humans

The wood mouse Apodemus sylvaticus is an opportunistic rodent that is found throughout most of the European mainland. It is present on many islands around the margins of the continent and in northern Africa. The species has been the subject of previous phylogeographic studies but these have focussed on the more southerly part of its range. A substantial number of new samples, many of them from the periphery of the species’ range, contribute to an exceptional dataset comprising 981 mitochondrial cytochrome b sequences. These new data provide sufficient resolution to transform our understanding of the species’ survival through the last glaciation and its subsequent re-colonisation of the continent. The deepest genetic split we found is in agreement with previous studies and runs from the Alps to central Ukraine, but we further distinguish two separate lineages in wood mice to the north and west of this line. It is likely that this part of Europe was colonised from two refugia, putatively located in the Iberian peninsula and the Dordogne or Carpathian region. The wood mouse therefore joins the growing number of species with extant populations that appear to have survived the Last Glacial Maximum in northern refugia, rather than solely in traditionally recognised refugial locations in the southern European peninsulas. Furthermore, the existence of a northern refugium for the species was predicted in a study of mitochondrial variation in a specific parasite of the wood mouse, demonstrating the potential value of data from parasites to phylogeographic studies. Lastly, the presence of related haplotypes in widely disparate locations, often on islands or separated by substantial bodies of water, demonstrates the propensity of the wood mouse for accidental human-mediated transport

Systematics of Round-Eared Bats (Tonatia and Lophostoma) Based on Nuclear and Mitochondrial DNA Sequences.

We examined the systematics of round-eared bats (Tonatia and Lophostoma) using sequence data from the nuclear recombination activator gene-2 (Rag2) gene and the mitochondrial valine transfer RNA, 12S ribosomal RNA (rRNA), and 16S rRNA. Some analyses of the mitochondrial and combined data sets indicate that round-eared bats may be paraphyletic relative to the genera Phyllostomus, Phylloderma, and Mimon. Both nuclear and mitochondrial data sets indicate substantial genetic divergence between Tonatia and Lophostoma, and neither data set unambiguously demonstrates monophyly of round-eared bats. However, our analyses cannot exclude the possibility that round-eared bats form a monophyletic lineage that separated anciently into Tonatia and Lophostoma. Within the Tonatia lineage, T. bidens and T. saurophila are sister taxa but are divergent for both nuclear and mitochondrial sequences. Nuclear data suggest that L. silvicolum may be paraphyletic, as currently recognized, because L. evotis appears within this clade