Epidemiological characteristics of human-infective RNA viruses

Woolhouse, Mark; Brierley, Liam

doi:10.1038/sdata.2018.17

Cited by 86 publications

(98 citation statements)

References 12 publications

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“…We chose RdRPs from human-infective viruses based on the list provided by Woolhouse & Brierley [8]. Given the global medical importance of AIDS, we also included Lentivirus reverse transcriptases (RTs) for analysis.…”

Section: Taxonomy Searchmentioning

confidence: 99%

Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling

Mead

Lunagómez

Gatherer

2019

Journal of Molecular Graphics and Modelling

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a b s t r a c tThe protein sequence-structure gap results from the contrast between rapid, low-cost deep sequencing, and slow, expensive experimental structure determination techniques. Comparative homology modelling may have the potential to close this gap by predicting protein structure in target sequences using existing experimentally solved structures as templates. This paper presents the first use of force-directed graphs for the visualization of sequence space in two dimensions, and applies them to the choice of suitable RNA-dependent RNA polymerase (RdRP) target-template pairs within human-infective RNA virus genera. Measures of centrality in protein sequence space for each genus were also derived and used to identify centroid nearest-neighbour sequences (CNNs) potentially useful for production of homology models most representative of their genera. Homology modelling was then carried out for targettemplate pairs in different species, different genera and different families, and model quality assessed using several metrics. Reconstructed ancestral RdRP sequences for individual genera were also used as templates for the production of ancestral RdRP homology models. High quality ancestral RdRP models were consistently produced, as were good quality models for target-template pairs in the same genus. Homology modelling between genera in the same family produced mixed results and inter-family modelling was unreliable. We present a protocol for the production of optimal RdRP homology models for use in further experiments, e.g. docking to discover novel anti-viral compounds. (219 words)

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Section: Taxonomy Searchmentioning

confidence: 99%

Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling

Mead

Lunagómez

Gatherer

2019

Journal of Molecular Graphics and Modelling

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“…According to a survey by Woolhouse et. al, the number of newly identified RNA viruses is changing from 1,899 in 2005 to 5,561 in 2018, which is 3 times of increase [3]. Largescale RNA virus sequencing projects using nextgeneration sequencing technologies have been conducted for different species.…”

Section: Introductionmentioning

confidence: 99%

CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning

Shang

Sun

2020

Preprint

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ABSTRARCTThe fast accumulation of viral metagenomic data has contributed significantly to new RNA virus discovery. However, the short read size, complex composition, and large data size can all make taxonomic analysis difficult. In particular, commonly used alignment-based methods are not ideal choices for detecting new viral species. In this work, we present a novel hierarchical classification model named CHEER, which can conduct read-level taxonomic classification from order to genus for new species. By combining k-mer embedding-based encoding, hierarchically organized CNNs, and carefully trained rejection layer, CHEER is able to assign correct taxonomic labels for reads from new species. We tested CHEER on both simulated and real sequencing data. The results show that CHEER can achieve higher accuracy than popular alignment-based and alignment-free taxonomic assignment tools. The source code, scripts, and pre-trained parameters for CHEER are available via GitHub: https://github.com/KennthShang/CHEER.

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“…2 RNA viruses are a major threat to human health, and severe acute respiratory syndrome (SARS) coronavirus, Ebola virus and Middle East respiratory syndrome (MERS) coronavirus are recently known to cause pandemics. 3 Of the discovered virus species, 214 viruses are known human-infective RNA viruses and 9 viruses are retroviruses (Table 1). 3 The human-infective retroviruses are human T-lymphotropic viruses (HTLV), human immunodeficiency viruses (HIV) and simian foamy viruses (SFV), and consist of 3 genuses (Deltaretrovirus, Lentivirus and Spumavirus, respectively; Table 1).…”

Section: Introductionmentioning

confidence: 99%

“…3 Of the discovered virus species, 214 viruses are known human-infective RNA viruses and 9 viruses are retroviruses (Table 1). 3 The human-infective retroviruses are human T-lymphotropic viruses (HTLV), human immunodeficiency viruses (HIV) and simian foamy viruses (SFV), and consist of 3 genuses (Deltaretrovirus, Lentivirus and Spumavirus, respectively; Table 1). The range of hosts of retroviruses is narrow, and HIV can be acquired only from humans although HTLV and SFV are from suspected zoonotic origin and intraspecies transmission to humans after first infection in nonhuman primates.…”

Section: Introductionmentioning

confidence: 99%

“…The range of hosts of retroviruses is narrow, and HIV can be acquired only from humans although HTLV and SFV are from suspected zoonotic origin and intraspecies transmission to humans after first infection in nonhuman primates. 3,4 Of the human genome, 5-8% are endogenous retroviruses derived from viral sequences with similarity to the infectious retroviruses. Understanding the endogenous retroviruses is clinically important because the accumulation of viral sequences has created the current human genome, and it can cause diseases associated with endogenous retroviruses.…”

Section: Introductionmentioning

confidence: 99%

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Evolutionary Medicine of Retroviruses in the Human Genome

Katsura

Asai

2019

The American Journal of the Medical Sciences

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Humans are infected with many viruses, and the immune system mostly removes viruses and the infected cells. However, certain viruses have entered the human genome. Of the human genome, »45% is composed of transposable elements (long interspersed nuclear elements [LINEs], short interspersed nuclear elements [SINEs] and transposons) and 5-8% is derived from viral sequences with similarity to infectious retroviruses. If integration of retrovirus occurs in a germline, the integrated viral sequences are heritable. Accumulation of viral sequences has created the current human genome. This article summarizes recent studies of retroviruses in humans and bridges clinical fields and evolutionary genetics. First, we report the repertories of human-infective retroviruses. Second, we review endogenous retroviruses in the human genome and diseases associated with endogenous retroviruses. Third, we discuss the biological functions of endogenous retroviruses and propose the concept of accelerated human evolution via viruses. Finally, we present perspectives of virology in the field of evolutionary medicine.

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Epidemiological characteristics of human-infective RNA viruses

Cited by 86 publications

References 12 publications

Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling

Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling

CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning

Evolutionary Medicine of Retroviruses in the Human Genome

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