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Open AccessJournal ArticleDOI

Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution

TLDR
The sequences of six novel chapparvoviruses identified through both metagenomic sampling of bat tissues and in silico screening of published vertebrate genome assemblies group together as a robustly supported monophyletic clade in phylogenetic trees.
Abstract
Chapparvoviruses are a highly divergent group of parvoviruses (family Parvoviridae) that have recently been identified via metagenomic sampling of animal faeces. Here, we report the sequences of six novel chapparvoviruses identified through both metagenomic sampling of bat tissues and in silico screening of published vertebrate genome assemblies. The novel chapparvoviruses share several distinctive genomic features and group together as a robustly supported monophyletic clade in phylogenetic trees. Our data indicate that chapparvoviruses have a broad host range in vertebrates and a global distribution.

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Reorganizing the family Parvoviridae: a revised taxonomy independent of the canonical approach based on host association.

TL;DR: A new and updated system for parvovirus classification is presented, which includes the introduction of a third subfamily, Hamaparvovirinae, resolves the paraphyly within genus Ambidensovirus, and introduces new genera and species into the subfamily ParvovIRinae.
Journal ArticleDOI

An Ancient Lineage of Highly Divergent Parvoviruses Infects both Vertebrate and Invertebrate Hosts.

TL;DR: The findings demonstrate that the ChPV lineage infects an exceptionally broad range of host species, including both vertebrates and invertebrates, and suggests that transmission between distantly related host species may have occurred in the past and that the Parvoviridae family can no longer be divided based on host affiliation.
Journal ArticleDOI

Virome heterogeneity and connectivity in waterfowl and shorebird communities.

TL;DR: Complex virome structures across host species that co-exist in multi-species aggregations are demonstrated and are indicative of both virome connectivity (host sharing) and heterogeneity (host specificity).
Journal ArticleDOI

Faecal Virome Analysis of Wild Animals from Brazil.

TL;DR: It is demonstrated that the metagenomics approach applied in this work was effective for identification of known and putative new viruses in faeces samples from Brazilian Cerrado fauna.
References
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Journal ArticleDOI

Basic Local Alignment Search Tool

TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
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MUSCLE: a multiple sequence alignment method with reduced time and space complexity

TL;DR: MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs, and a new option, MUSCLE-fast, designed for high-throughput applications.
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ProtTest 3

TL;DR: A high-performance computing (HPC) version of ProtTest that can be executed in parallel in multicore desktops and clusters, called ProtTest 3, includes new features and extended capabilities.
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