Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics

Porter, Ashleigh F.; Shī, Mǎng; Eden, John‐Sebastian; Zhang, Yongzhen; Holmes, Edward C.

doi:10.3390/v11121092

Cited by 19 publications

(14 citation statements)

References 66 publications

(100 reference statements)

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“…Interestingly, however, one of viruses identified in this study, reagent-associated CRESS-like virus 4, is most closely related to Avon-Heathcote Estuary associated circular virus 3, previously identified as a reagent-associated virus [42]. In addition, the seven novel CRESS-like sequences identified here were related to previously identified reagent-associated viruses, including those identified by Asplund et al (highlighted in blue, Figure 2) [9], as well as Sandworm circovirus similarly proposed to be a reagent contaminant [43]. This strongly suggests that all these sequences are likely associated with laboratory reagents.…”

Section: Discussionsupporting

confidence: 73%

Metagenomic identification of viral sequences in laboratory reagents

Porter

Cobbin

et al. 2021

Preprint

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Metagenomic next–generation sequencing has transformed the discovery and diagnosis of infectious disease, with the power to characterize the complete infectome (bacteria, viruses, fungi, parasites) of an individual host organism. However, the identification of novel pathogens has been complicated by widespread microbial contamination in commonly used laboratory reagents. Using total RNA sequencing (metatranscriptomics) we documented the presence of contaminant viral sequences in multiple libraries of blank negative control sequencing libraries that comprise a sterile water and reagent mix. Accordingly, we identified 14 viral sequences in 7 negative control sequencing libraries. As in previous studies, several circular replication–associated protein encoding (CRESS) DNA virus–like sequences were recovered in the blank libraries, as well as contaminating sequences from the RNA virus families Totiviridae, Tombusviridae and Lentiviridae. These data suggest that the contamination of common laboratory reagents is likely widespread and can comprise a wide variety of viruses.

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Section: Discussionsupporting

confidence: 73%

Metagenomic identification of viral sequences in laboratory reagents

Porter

Cobbin

et al. 2021

Preprint

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“…2019 ; Pettersson et al. 2019 ; Porter et al. 2019 ), we still have an incomplete understanding of the factors that structure viromes.…”

Section: Introductionmentioning

confidence: 99%

Virome composition in marine fish revealed by meta-transcriptomics

et al. 2021

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Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so provide an ideal model system to study the factors that shape virome compositions and their evolution. We characterised the viromes of 19 wild-caught species of marine fish using total RNA sequencing (meta-transcriptomics) combined with analyses of sequence and protein structural homology to identify divergent viruses that often evade characterisation. From this, we identified 25 new vertebrate-associated viruses and a further 22 viruses likely associated with fish diet or their microbiomes. The vertebrate-associated viruses identified here included the first fish virus in the Matonaviridae (single-strand, negative-sense RNA virus). Other viruses fell within the Astroviridae, Picornaviridae, Arenaviridae, Reoviridae, Hepadnaviridae, Paramyxoviridae, Rhabdoviridae, Hantaviridae, Filoviridae and Flaviviridae and were sometimes phylogenetically distinct from known fish viruses. We also show how key metrics of virome composition—viral richness, abundance and diversity—can be analysed along with host ecological and biological factors as a means to understand virus ecology. Accordingly, these data suggest that that the vertebrate-associated viromes of the fish sampled here are predominantly shaped by the phylogenetic history (i.e. taxonomic order) of their hosts, along with several biological factors including water temperature, habitat depth, community diversity and swimming behaviour. No such correlations were found for viruses associated with porifera, molluscs, arthropods, fungi and algae, that are unlikely to replicate in fish hosts. Overall, these data indicate that fish harbour particularly large and complex viromes and the vast majority of fish viromes are undescribed.

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“…These methods provide an unbiased view of the virome within a host, expand our knowledge of viral diversity, and fill in the "gaps" between many higher virus taxa [1][2][3][4]. Among various metagenomic methods used for virus discovery, metatranscriptomics (i.e., total RNA sequencing) represents a simple but efficient approach that not only transforms our view of the genomic diversity of RNA viruses in a wide range of hosts [5][6][7], but also expands our knowledge of the diversity of DNA viruses [8][9][10][11]. Indeed, after reanalyzing the 92 metatranscriptomics data from invertebrate RNA sequencing, Porter et al [9] were able to reveal DNA viruses from at least 29 families, including 19 novel species from both large and small DNA virus families, and with good genome coverage.…”

Section: Introductionmentioning

confidence: 99%

“…Among various metagenomic methods used for virus discovery, metatranscriptomics (i.e., total RNA sequencing) represents a simple but efficient approach that not only transforms our view of the genomic diversity of RNA viruses in a wide range of hosts [5][6][7], but also expands our knowledge of the diversity of DNA viruses [8][9][10][11]. Indeed, after reanalyzing the 92 metatranscriptomics data from invertebrate RNA sequencing, Porter et al [9] were able to reveal DNA viruses from at least 29 families, including 19 novel species from both large and small DNA virus families, and with good genome coverage. Furthermore, with RNA sequencing, some DNA viruses can reach extremely high abundance levels [8], reflecting active RNA transcription and potentially acute infection within the host.…”

Section: Introductionmentioning

confidence: 99%

Discovery and Characterization of Actively Replicating DNA and Retro-Transcribing Viruses in Lower Vertebrate Hosts Based on RNA Sequencing

Chen

Shī

2021

Viruses

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In a previous study, a metatranscriptomics survey of RNA viruses in several important lower vertebrate host groups revealed huge viral diversity, transforming the understanding of the evolution of vertebrate-associated RNA virus groups. However, the diversity of the DNA and retro-transcribing viruses in these host groups was left uncharacterized. Given that RNA sequencing is capable of revealing viruses undergoing active transcription and replication, we collected previously generated datasets associated with lower vertebrate hosts, and searched them for DNA and retro-transcribing viruses. Our results revealed the complete genome, or “core gene sets”, of 18 vertebrate-associated DNA and retro-transcribing viruses in cartilaginous fishes, ray-finned fishes, and amphibians, many of which had high abundance levels, and some of which showed systemic infections in multiple organs, suggesting active transcription or acute infection within the host. Furthermore, these new findings recharacterized the evolutionary history in the families Hepadnaviridae, Papillomaviridae, and Alloherpesviridae, confirming long-term virus–host codivergence relationships for these virus groups. Collectively, our results revealed reliable and sufficient information within metatranscriptomics sequencing to characterize not only RNA viruses, but also DNA and retro-transcribing viruses, and therefore established a key methodology that will help us to understand the composition and evolution of the total “infectome” within a diverse range of vertebrate hosts.

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Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics

Cited by 19 publications

References 66 publications

Metagenomic identification of viral sequences in laboratory reagents

Metagenomic identification of viral sequences in laboratory reagents

Virome composition in marine fish revealed by meta-transcriptomics

Discovery and Characterization of Actively Replicating DNA and Retro-Transcribing Viruses in Lower Vertebrate Hosts Based on RNA Sequencing

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