Detecting the emergence of novel, zoonotic viruses pathogenic to humans

Rosenberg, Ronald

doi:10.1007/s00018-014-1785-y

Cited by 77 publications

(68 citation statements)

References 49 publications

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“…1) and require choosing between extracting DNA and RNA simultaneously or independently. Since (re)emerging viral threats are mainly caused by RNA viruses [5,44], viral nucleic acid isolation can be performed using TRIzol LS (Life Technologies) or reagents designed to obtain high quality RNA molecules in high yields. Following viral particles lysis and nucleic acid precipitation steps, viral genomic RNAs are purified using a spin column.…”

Section: Sample Preparationmentioning

confidence: 99%

Viral metagenomics and blood safety

Sauvage

Éloit

2016

Transfusion Clinique et Biologique

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The characterization of the human blood-associated viral community (also called blood virome) is essential for epidemiological surveillance and to anticipate new potential threats for blood transfusion safety. Currently, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) can be considered as under control in high-resource countries. However, other viruses unknown or unsuspected may be transmitted to recipients by blood-derived products. This is particularly relevant considering that a significant proportion of transfused patients are immunocompromised and more frequently subjected to fatal outcomes. Several measures to prevent transfusion transmission of unknown viruses have been implemented including the exclusion of at-risk donors, leukocyte reduction of donor blood, and physicochemical treatment of the different blood components. However, up to now there is no universal method for pathogen inactivation, which would be applicable for all types of blood components and, equally effective for all viral families. In addition, among available inactivation procedures of viral genomes, some of them are recognized to be less effective on non-enveloped viruses, and inadequate to inactivate higher viral titers in plasma pools or derivatives. Given this, there is the need to implement new methodologies for the discovery of unknown viruses that may affect blood transfusion. Viral metagenomics combined with High Throughput Sequencing appears as a promising approach for the identification and global surveillance of new and/or unexpected viruses that could impair blood transfusion safety.

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Section: Sample Preparationmentioning

confidence: 99%

Viral metagenomics and blood safety

Sauvage

Éloit

2016

Transfusion Clinique et Biologique

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“…Generally, a new pathogen would not be identified until it caused epidemics or pandemics. Many viruses that may have been introduced into human populations remain undiscovered (Rosenberg, ). Traditional diagnostic methods such as polymerase chain reaction, immunological assays and pan‐viral microarrays are inadequate for the quick identification of novel human‐infecting viruses (Corman et al, ; Wootton et al, ).…”

Section: Introductionmentioning

confidence: 99%

Rapid identification of human‐infecting viruses

Zhang

Cai

Tan

et al. 2019

Transbound Emerg Dis

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Viruses have caused much mortality and morbidity to humans and pose a serious threat to global public health. The virome with the potential of human infection is still far from complete. Novel viruses have been discovered at an unprecedented pace as the rapid development of viral metagenomics. However, there is still a lack of methodology for rapidly identifying novel viruses with the potential of human infection. This study built several machine learning models to discriminate human‐infecting viruses from other viruses based on the frequency of k‐mers in the viral genomic sequences. The k‐nearest neighbor (KNN) model can predict the human‐infecting viruses with an accuracy of over 90%. The performance of this KNN model built on the short contigs (≥1 kb) is comparable to those built on the viral genomes. We used a reported human blood virome to further validate this KNN model with an accuracy of over 80% based on very short raw reads (150 bp). Our work demonstrates a conceptual and generic protocol for the discovery of novel human‐infecting viruses in viral metagenomics studies.

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“…RNA viruses have considerable potential to adapt to new environmental conditions and to overcome host restrictions ( 10 ). Until now, the host tropism of PPgV has not been investigated in detail.…”

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confidence: 99%