RESUMO
In 2015, we identified an avian hepatitis B virus associated with hepatitis in a group of captive elegant-crested tinamous (Eudromia elegans) in Germany. The full-length genome of this virus shares <76% sequence identity with other avihepadnaviruses. The virus may therefore be considered a new extant avian hepadnavirus.
Assuntos
Doenças das Aves/epidemiologia , Genoma Viral , Infecções por Hepadnaviridae/veterinária , Hepadnaviridae/genética , Hepatite Viral Animal/epidemiologia , Proteínas Virais/genética , Animais , Animais de Zoológico , Evolução Biológica , Doenças das Aves/patologia , Doenças das Aves/virologia , Extinção Biológica , Alemanha/epidemiologia , Hepadnaviridae/classificação , Hepadnaviridae/isolamento & purificação , Infecções por Hepadnaviridae/epidemiologia , Infecções por Hepadnaviridae/patologia , Infecções por Hepadnaviridae/virologia , Hepatite Viral Animal/patologia , Hepatite Viral Animal/virologia , Especificidade de Hospedeiro , Humanos , Fígado/patologia , Fígado/virologia , Fases de Leitura Aberta , Paleógnatas/virologia , FilogeniaRESUMO
Circoviruses are circular, non-enveloped, single-stranded DNA viruses around 2000 nucleotides (nt) in length and include the pathogenic species, Porcine circovirus 1 and Beak and feather disease virus, capable of causing significant morbidity and mortality. This group of viruses may be robust to degradation by external environments, and avian circoviruses are known to move between closely related hosts. Using a de novo metagenomic approach, followed by confirmatory PCR, we identify for the first time a circular Rep-encoding single-stranded (CRESS) DNA virus in New Zealand kiwi, Apteryx spp., derived from faecal matter of the rowi kiwi (A. rowi) showing signs of verminous dermatitis. The entire 2085 nt genome was cloned and sequenced and contains both capsid and replicase genes, as well as a conserved 9 nt motif. Phylogenetic analyses place it within Circoviridae, adjacent to other environmental CRESS-DNA viruses, and most closely related to badger circovirus-like virus (Meles meles circovirus-like virus). As the rowi is the most critically endangered kiwi, it is vital to understand the role of rowi kiwi circovirus-like virus as a possible pathogen and also any potential cross-species transmission.
Assuntos
Infecções por Circoviridae/virologia , Circovirus/genética , Genoma Viral/genética , Paleógnatas/virologia , Animais , Proteínas do Capsídeo/genética , Circoviridae/genética , DNA de Cadeia Simples/genética , DNA Viral/genética , Nova Zelândia , Fases de Leitura Aberta/genética , FilogeniaRESUMO
Applying high-throughput sequencing to pathogen discovery is a relatively new field, the objective of which is to find disease-causing agents when little or no background information on disease is available. Key steps in the process are the generation of millions of sequence reads from an infected tissue sample, followed by assembly of these reads into longer, contiguous stretches of nucleotide sequences, and then identification of the contigs by matching them to known databases, such as those stored at GenBank or Ensembl. This technique, that is, de novo metagenomics, is particularly useful when the pathogen is viral and strong discriminatory power can be achieved. However, recently, we found that striking differences in results can be achieved when different assemblers were used. In this study, we test formally the impact of five popular assemblers (MIRA, VELVET, METAVELVET, SPADES, and OMEGA) on the detection of a novel virus and assembly of its whole genome in a data set for which we have confirmed the presence of the virus by empirical laboratory techniques, and compare the overall performance between assemblers. Our results show that if results from only one assembler are considered, biologically important reads can easily be overlooked. The impacts of these results on the field of pathogen discovery are considered.