Printed in Great Britain Genome sequence analysis of Tamana bat virus and its relationship with the genus Flavivirus

Tamana bat virus (TABV, isolated from the bat Pteronotus parnellii) is currently classified as a tentative species in the genus Flavivirus. We report here the determination and analysis of its complete coding sequence. Low but significant similarity scores between TABV and memberviruses of the genus Flavivirus were identified in the amino acid sequences of the structural, NS3 and NS5 genes. A series of cysteines located in the envelope protein and the most important enzymatic domains of the virus helicase/NTPase, methyltransferase and RNA-dependent RNA polymerase were found to be highly conserved. In the serine-protease domain, the catalytic sites were conserved, but variations in sequence were found in the putative substrate-binding sites, implying possible differences in the protease specificity. In accordance with this finding, the putative cleavage sites of the TABV polyprotein by the virus protease are substantially different from those of flaviviruses. The phylogenetic position of TABV could not be determined precisely, probably due to the extremely significant genetic divergence from other member-viruses of the family Flaviviridae. However, analysis based on both genetic distances and maximum-likelihood confirmed that TABV is more closely related to the flaviviruses than to the other genera. These findings have implications for the evolutionary history and taxonomic classification of the family as a whole : (i) the possibility that flaviviruses were derived from viruses infecting mammals rather than from mosquito viruses cannot be excluded ; (ii) using the current criteria for the definition of genera in the family Flaviviridae, TABV should be assigned to a new genus

Taming of the shrewd: novel eukaryotic genes from RNA viruses

Genomes of several yeast species contain integrated DNA copies of complete genomes or individual genes of non-retroviral double-strand RNA viruses as reported in a recent BMC Biology article by Taylor and Bruenn. The integrated virus-specific sequences are at least partially expressed and seem to evolve under pressure of purifying selection, indicating that these are functional genes. Together with similar reports on integrated copies of some animal RNA viruses, these results suggest that integration of DNA copies of non-reverse-transcribing RNA viruses might be much more common than previously thought. The integrated copies could contribute to acquired immunity to the respective viruses

Unexpected Inheritance: Multiple Integrations of Ancient Bornavirus and Ebolavirus/Marburgvirus Sequences in Vertebrate Genomes

Vertebrate genomes contain numerous copies of retroviral sequences, acquired over the course of evolution. Until recently they were thought to be the only type of RNA viruses to be so represented, because integration of a DNA copy of their genome is required for their replication. In this study, an extensive sequence comparison was conducted in which 5,666 viral genes from all known non-retroviral families with single-stranded RNA genomes were matched against the germline genomes of 48 vertebrate species, to determine if such viruses could also contribute to the vertebrate genetic heritage. In 19 of the tested vertebrate species, we discovered as many as 80 high-confidence examples of genomic DNA sequences that appear to be derived, as long ago as 40 million years, from ancestral members of 4 currently circulating virus families with single strand RNA genomes. Surprisingly, almost all of the sequences are related to only two families in the Order Mononegavirales: the Bornaviruses and the Filoviruses, which cause lethal neurological disease and hemorrhagic fevers, respectively. Based on signature landmarks some, and perhaps all, of the endogenous virus-like DNA sequences appear to be LINE element-facilitated integrations derived from viral mRNAs. The integrations represent genes that encode viral nucleocapsid, RNA-dependent-RNA-polymerase, matrix and, possibly, glycoproteins. Integrations are generally limited to one or very few copies of a related viral gene per species, suggesting that once the initial germline integration was obtained (or selected), later integrations failed or provided little advantage to the host. The conservation of relatively long open reading frames for several of the endogenous sequences, the virus-like protein regions represented, and a potential correlation between their presence and a species' resistance to the diseases caused by these pathogens, are consistent with the notion that their products provide some important biological advantage to the species. In addition, the viruses could also benefit, as some resistant species (e.g. bats) may serve as natural reservoirs for their persistence and transmission. Given the stringent limitations imposed in this informatics search, the examples described here should be considered a low estimate of the number of such integration events that have persisted over evolutionary time scales. Clearly, the sources of genetic information in vertebrate genomes are much more diverse than previously suspected

No Evidence of Gouléako and Herbert Virus Infections in Pigs, Côte d’Ivoire and Ghana

A recent report suggested that 2 novel bunyaviruses discovered in insects in Côte d’Ivoire caused lethal disease in swine in South Korea. We conducted cell culture studies and tested serum from pigs exposed to mosquitoes in Côte d’Ivoire and Ghana and found no evidence for infection in pigs

Isolates of Liao Ning Virus from Wild-Caught Mosquitoes in the Xinjiang Province of China in 2005

Liao ning virus (LNV) is related to Banna virus, a known human-pathogen present in south-east Asia. Both viruses belong to the genus Seadornavirus, family Reoviridae. LNV causes lethal haemorrhage in experimentally infected mice. Twenty seven isolates of LNV were made from mosquitoes collected in different locations within the Xinjiang province of north-western China during 2005. These mosquitoes were caught in the accommodation of human patients with febrile manifestations, or in animal barns where sheep represent the main livestock species. The regions where LNV was isolated are affected by seasonal encephalitis, but are free of Japanese encephalitis (JE). Genome segment 10 (Seg-10) (encoding cell-attachment and serotype-determining protein VP10) and Seg-12 (encoding non-structural protein VP12) were sequenced for multiple LNV isolates. Phylogenetic analyses showed a less homogenous Seg-10 gene pool, as compared to segment 12. However, all of these isolates appear to belong to LNV type-1. These data suggest a relatively recent introduction of LNV into Xinjiang province, with substitution rates for LNV Seg-10 and Seg-12, respectively, of 2.29×10−4 and 1.57×10−4 substitutions/nt/year. These substitution rates are similar to those estimated for other dsRNA viruses. Our data indicate that the history of LNV is characterized by a lack of demographic fluctuations. However, a decline in the LNV population in the late 1980s - early 1990s, was indicated by data for both Seg-10 and Seg-12. Data also suggest a beginning of an expansion in the late 1990s as inferred from Seg-12 skyline plot

Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses

Ancient hepadnavirus sequences found in bird genomes reveal that this family of viruses, which includes the human hepatitis B virus, is much older than previously thought

Carving the romantic lied : poetic of the Goethezeit ballad

Lorsque l’on se penche sur les poèmes appelés ballades, objets d’une furieuse vogue dans le monde germanique depuis le Sturm und Drang, on se heurte partout à l’absence d’accord sur ce qui fait leur spécificité. C’est en partie dans cet espace poético-musical protéiforme qu’est forgé le lied romantique. Franz Schubert (1797-1828) passe ses premières années de compositeur à mettre en musique de longues ballades, et y revient jusqu’à la fin de sa vie ; Carl Loewe (1796-1869) passe maître de cet art. La ductilité du genre, sa résistance aux tentatives de définition sur le double terrain des lettres et de la musique (Sulzer 1771-1774, Koch 1802, Hegel 1818-1830, Häuser 1833…) mettent en péril sa propre pérennité, mais font aussi de lui un extraordinaire terrain d’expérimentation pour la lyrique musicale en effervescence. Il entre en résonance avec bien des enjeux de la musique du XIXe siècle, parmi lesquels la pratique orale des interprètes, récitants et chanteurs, la question de la narration musicale, et les passerelles entre musique de salon et scène lyrique, entre domaine vocal et domaine instrumental. Cette thèse souhaite contribuer à éclairer le devenir du Kunstlied à travers le prisme d’un de ses lieux privilégiés d’élaboration. Avec la ballade, cet étrange hybride de récit sans conteur identifiable, de drame sans scène et de musique, les dimensions du traditionnel Lied germanique s’élargissent jusqu’à l’émergence du Kunstlied ; mieux, elle fait d’entrée de jeu éclater l’unité émotionnelle de ce dernier. Notre recherche retrace ce parcours imprévisible et les questions qu’il soulève, pour mieux comprendre, non pas l’objet abouti que serait « le lied romantique », mais plutôt le passionnant travail de création artistique, le progressif modelage d’un objet musical, entre-deux des genres, dans ses multiples formes au fil du temps.When we look at the poems called ballads, which have been furiously popular in the Germanic world since the Sturm und Drang, we encounter a general lack of agreement on their specificity. The Romantic Lied was partly forged in this multifaceted poetic-musical space. Franz Schubert (1797-1828) spent his early composing years setting long ballads to music, and was to return to do so until the end of his life; Carl Loewe (1796-1869) became a master of this art. The ductility of the genre and its resistance to all attempts at defining it in the two fields of literature and music (Sulzer 1771-1774, Koch 1802, Hegel 1818-1830, Häuser 1833…) jeopardize its own durability, but also make it an extraordinary experimental field for the vibrant musical lyricism. It is in tune with many of the issues at stake in 19th-century music, including the vocal practice of performers, reciters and singers, the issue of musical narration, and the connections between salon music and lyric stage performance, between the vocal and instrumental realms. This dissertation attempts to shed light on the becoming of Kunstlied through the prism of one of its key development settings. The ballad, a strange hybrid of storytelling without an identifiable storyteller, of music and stageless drama, broadens the dimensions of the traditional German Lied until the emergence of Kunstlied; better still, it shatters the emotional unity of the latter from the outset. Our research retraces this unpredictable process and the questions it raises, in order to better understand not the accomplished object that would be “the romantic Lied”, but rather the exciting work of artistic creation, the progressive modelling of a musical object, between the genres, in its multiple expressions over time