Diversification of mammalian deltaviruses by host shifting

Bergner, Laura M.; Orton, Richard; Broos, Alice; Tello, Carlos; Becker, Daniel J.; Carrera, Jorge; Patel, Arvind H.; Biek, Roman; Streicker, Daniel G.

doi:10.1101/2020.06.17.156745

Cited by 11 publications

(12 citation statements)

References 81 publications

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“…As described above, ovDeV and mmDeV are close relatives of human HDVs, suggesting that HDVs arose from other mammalian deltaviruses. Recent studies on the phylogeny of bat deltaviruses support our findings and conclusions ( Bergner et al. 2020 ; Edgar et al.…”

Section: Discussionsupporting

confidence: 90%

Identification of novel avian and mammalian deltaviruses provides new insights into deltavirus evolution

et al. 2021

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Hepatitis delta virus (HDV) is a satellite virus that requires hepadnavirus envelope proteins for its transmission. Although recent studies identified HDV-related deltaviruses in certain animals, the evolution of deltaviruses, such as the origin of HDV and the mechanism of its coevolution with its helper viruses, is unknown, mainly because of the phylogenetic gaps among deltaviruses. Here we identified novel deltaviruses of passerine birds, woodchucks, and white-tailed deer by extensive database searches and molecular surveillance. Phylogenetic and molecular epidemiological analyses suggest that HDV originated from mammalian deltaviruses and the past interspecies transmission of mammalian and passerine deltaviruses. Further, metaviromic and experimental analyses suggest that the satellite-helper relationship between HDV and hepadnavirus was established after the divergence of the HDV lineage from non-HDV mammalian deltaviruses. Our findings enhance our understanding of deltavirus evolution, diversity, and transmission, indicating the importance of further surveillance for deltaviruses.

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Section: Discussionsupporting

confidence: 90%

Identification of novel avian and mammalian deltaviruses provides new insights into deltavirus evolution

et al. 2021

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“…We also mined publicly available metagenomic and transcriptomic datasets for evidence of a betacoronavirus infection. 55 , 56 , 57 However, no published libraries contained evidence of betacoronaviruses ( appendix p 15 ). Lastly, we analysed the wildlife testing data from the US Agency for International Development Emerging Pandemic Threats PREDICT programme, collected from 2009 to 2019, which was publicly released in June, 2021, and includes many betacoronaviruses that were discovered during the programme's run but have only published and identified down to the genus level in the full release.…”

Section: Model Validationmentioning

confidence: 99%

Optimising predictive models to prioritise viral discovery in zoonotic reservoirs

et al. 2022

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Despite the global investment in One Health disease surveillance, it remains difficult and costly to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can guide sampling target prioritisation, but the predictions from any given model might be highly uncertain; moreover, systematic model validation is rare, and the drivers of model performance are consequently under-documented. Here, we use the bat hosts of betacoronaviruses as a case study for the data-driven process of comparing and validating predictive models of probable reservoir hosts. In early 2020, we generated an ensemble of eight statistical models that predicted host–virus associations and developed priority sampling recommendations for potential bat reservoirs of betacoronaviruses and bridge hosts for SARS-CoV-2. During a time frame of more than a year, we tracked the discovery of 47 new bat hosts of betacoronaviruses, validated the initial predictions, and dynamically updated our analytical pipeline. We found that ecological trait-based models performed well at predicting these novel hosts, whereas network methods consistently performed approximately as well or worse than expected at random. These findings illustrate the importance of ensemble modelling as a buffer against mixed-model quality and highlight the value of including host ecology in predictive models. Our revised models showed an improved performance compared with the initial ensemble, and predicted more than 400 bat species globally that could be undetected betacoronavirus hosts. We show, through systematic validation, that machine learning models can help to optimise wildlife sampling for undiscovered viruses and illustrates how such approaches are best implemented through a dynamic process of prediction, data collection, validation, and updating.

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“…2019 ; Paraskevopoulou et al. 2020 ; Bergner et al. 2021 ) indicating that this atypical virus has a longer and more complex evolutionary history than previously thought.…”

Section: Introductionmentioning

confidence: 83%

Hepatitis delta virus-like circular RNAs from diverse metazoans encode conserved hammerhead ribozymes

et al. 2021

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Human hepatitis delta virus (HDV) is a unique infectious agent whose genome is composed of a small circular RNA. Recent data, however, have reported the existence of highly divergent HDV-like circRNAs in the transcriptomes of diverse vertebrate and invertebrate species. The HDV-like RNAs described in amniotes such as birds and reptiles encode self-cleaving RNA motifs or ribozymes similar to the ones present in the human HDV, whereas no catalytic RNA domains have been reported for the HDV-like circRNAs detected in metagenomic data from some amphibians, fish, and invertebrates. Herein, we describe the self-cleaving motifs of the HDV-like genomes reported in newts and fish, which belong to the characteristic class of HDV ribozymes. Surprisingly, HDV-like circRNAs from a toad and a termite show conserved type-III hammerhead ribozymes, which belong to an unrelated class of catalytic RNAs characteristic of plant genomes and plant subviral circRNAs, such as some viral satellites and viroids. Sequence analyses revealed the presence of very similar HDV-like hammerhead ribozymes encoded in two termite genomes, but also in the genomes of several dipteran species. In vitro transcriptions confirmed the cleaving activity for these motifs, with moderate rates of self-cleavage. These data indicate that all described HDV-like agents contain self-cleaving motifs from either the HDV or the hammerhead class. Autocatalytic ribozymes in HDV-like genomes could be regarded as interchangeable domains and may have arisen from cellular transcriptomes, although we still cannot rule out some other evolutionary explanations.

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Diversification of mammalian deltaviruses by host shifting

Cited by 11 publications

References 81 publications

Identification of novel avian and mammalian deltaviruses provides new insights into deltavirus evolution

Identification of novel avian and mammalian deltaviruses provides new insights into deltavirus evolution

Optimising predictive models to prioritise viral discovery in zoonotic reservoirs

Hepatitis delta virus-like circular RNAs from diverse metazoans encode conserved hammerhead ribozymes

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