Metagenomic identification of a novel anellovirus in Pacific harbor seal (Phoca vitulina richardsii) lung samples and its detection in samples from multiple years

Ng, Terry Fei Fan; Wheeler, Elizabeth; Greig, Denise J.; Waltzek, Thomas B.; Gulland, Frances M. D.; Breitbart, Mya

doi:10.1099/vir.0.029678-0

Cited by 68 publications

(63 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…RNA viral sequences were not observed in our data, and since the sequence coding the replication protein from this putative virus contained premature stop codons, similar sequences would have been excluded from our analyses. Sequences similar to those from the Anelloviridae, which occur in insects and mammals including California sea lions and Pacific harbor seals (Ng et al, 2011), were not found in our samples, suggesting that they were rare or too divergent to be assigned to the family. Viruses from the Parvoviridae family have linear genomes and would not be enriched by MDA, and were excluded from this analysis.…”

Section: Resultsmentioning

confidence: 80%

Previously unknown and highly divergent ssDNA viruses populate the oceans

2013

View full text Add to dashboard Cite

Single-stranded DNA (ssDNA) viruses are economically important pathogens of plants and animals, and are widespread in oceans; yet, the diversity and evolutionary relationships among marine ssDNA viruses remain largely unknown. Here we present the results from a metagenomic study of composite samples from temperate (Saanich Inlet, 11 samples; Strait of Georgia, 85 samples) and subtropical (46 samples, Gulf of Mexico) seawater. Most sequences (84%) had no evident similarity to sequenced viruses. In total, 608 putative complete genomes of ssDNA viruses were assembled, almost doubling the number of ssDNA viral genomes in databases. These comprised 129 genetically distinct groups, each represented by at least one complete genome that had no recognizable similarity to each other or to other virus sequences. Given that the seven recognized families of ssDNA viruses have considerable sequence homology within them, this suggests that many of these genetic groups may represent new viral families. Moreover, nearly 70% of the sequences were similar to one of these genomes, indicating that most of the sequences could be assigned to a genetically distinct group. Most sequences fell within 11 well-defined gene groups, each sharing a common gene. Some of these encoded putative replication and coat proteins that had similarity to sequences from viruses infecting eukaryotes, suggesting that these were likely from viruses infecting eukaryotic phytoplankton and zooplankton.

show abstract

Section: Resultsmentioning

confidence: 80%

Previously unknown and highly divergent ssDNA viruses populate the oceans

2013

View full text Add to dashboard Cite

show abstract

“…Viral nucleic acids were first nonspecifically amplified using random hexamers by rolling-circle amplification (Genomiphi; GE Healthcare) and then further amplified by specific primers designed to amplify the whole circular genome using inverse PCR (70,71). PCR amplicons were then Sanger sequenced.…”

Section: Methodsmentioning

confidence: 99%

High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

Marine

Wang

et al. 2012

J Virol

Self Cite

241

213

View full text Add to dashboard Cite

g Deep sequencing of untreated sewage provides an opportunity to monitor enteric infections in large populations and for highthroughput viral discovery. A metagenomics analysis of purified viral particles in untreated sewage from the United States (San Francisco, CA), Nigeria (Maiduguri), Thailand (Bangkok), and Nepal (Kathmandu) revealed sequences related to 29 eukaryotic viral families infecting vertebrates, invertebrates, and plants (BLASTx E score, <10 ؊4 ), including known pathogens (>90% protein identities) in numerous viral families infecting humans (Adenoviridae, Astroviridae, Caliciviridae, Hepeviridae, Parvoviridae, Picornaviridae, Picobirnaviridae, and Reoviridae), plants (Alphaflexiviridae, Betaflexiviridae, Partitiviridae, Sobemovirus, Secoviridae, Tombusviridae, Tymoviridae, Virgaviridae), and insects (Dicistroviridae, Nodaviridae, and Parvoviridae). The full and partial genomes of a novel kobuvirus, salivirus, and sapovirus are described. A novel astrovirus (casa astrovirus) basal to those infecting mammals and birds, potentially representing a third astrovirus genus, was partially characterized. Potential new genera and families of viruses distantly related to members of the single-stranded RNA picorna-like virus superfamily were genetically characterized and named Picalivirus, Secalivirus, Hepelivirus, Nedicistrovirus, Cadicistrovirus, and Niflavirus. Phylogenetic analysis placed these highly divergent genomes near the root of the picorna-like virus superfamily, with possible vertebrate, plant, or arthropod hosts inferred from nucleotide composition analysis. Circular DNA genomes distantly related to the plantinfecting Geminiviridae family were named Baminivirus, Nimivirus, and Niminivirus. These results highlight the utility of analyzing sewage to monitor shedding of viral pathogens and the high viral diversity found in this common pollutant and provide genetic information to facilitate future studies of these newly characterized viruses.

show abstract

“…2c). The amino acid sequences were aligned using Mafft 5.8 [2] with the E–INS–I alignment strategy and previously described parameters [5, 6]. A maximum-likelihood tree was created using RaxML based on the Mafft alignment with previously described parameters [6, 10].…”

mentioning

confidence: 99%

A divergent clade of circular single-stranded DNA viruses from pig feces

Cheung

Lager

et al. 2013

Arch Virol

View full text Add to dashboard Cite

Using metagenomics and molecular cloning methods, we characterized five novel small, circular viral genomes from pig feces that are distantly related to chimpanzee and porcine stool-associated circular viruses, (ChiSCV and PoSCV1). Phylogenetic analysis placed these viruses into a highly divergent clade of this rapidly growing new viral family. This new clade of viruses, provisionally named porcine stool-associated circular virus 2 and 3 (PoSCV2 and PoSCV3), encodes a stem–loop structure (presumably the origin of DNA replication) in the small intergenic region and a replication initiator protein commonly found in other biological systems that replicate their genomes via the rolling–circle mechanism. Furthermore, these viruses also exhibit three additional overlapping open reading frames in the large intergenic region between the capsid and replication initiator protein genes.

show abstract

Metagenomic identification of a novel anellovirus in Pacific harbor seal (Phoca vitulina richardsii) lung samples and its detection in samples from multiple years

Cited by 68 publications

References 41 publications

Previously unknown and highly divergent ssDNA viruses populate the oceans

Previously unknown and highly divergent ssDNA viruses populate the oceans

High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

A divergent clade of circular single-stranded DNA viruses from pig feces

Contact Info

Product

Resources

About