Next-generation sequencing technologies in diagnostic virology

Barzon, Luisa; Lavezzo, Enrico; Costanzi, G; Franchin, Elisa; Toppo, Stefano; Palù, Giorgio

doi:10.1016/j.jcv.2013.03.003

Cited by 112 publications

(92 citation statements)

References 32 publications

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“…The application of genomic and transcriptomic highthroughput sequencing technologies in clinical infections are likely to elucidate mechanisms of viral pathogenesis and antiviral therapy (97)(98)(99). There is no clear correlation, for example, of specific genotypes for UL55 (gB), UL73 (gN), UL144 (TNF-a receptor) or UL75 (gH) with clinical manifestations of disease (38,100).…”

Section: Genetics and Variability In Clinical Diseasementioning

confidence: 99%

The Cell Biology of Cytomegalovirus: Implications for Transplantation

Kaminski

Fishman

2016

American Journal of Transplantation

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Interpretation of clinical data regarding the impact of cytomegalovirus (CMV) infection on allograft function is complicated by the diversity of viral strains and substantial variability of cellular receptors and viral gene expression in different tissues. Variation also exists in nonspecific (monocytes and dendritic cells) and specific (NK cells, antibodies) responses that augment T cell antiviral activities. Innate immune signaling pathways and expanded pools of memory NK cells and cd T cells also serve to amplify host responses to infection. The clinical impact of specific memory T cell anti-CMV responses that cross-react with graft antigens and alloantigens is uncertain but appears to contribute to graft injury and to the abrogation of allograft tolerance. These responses are modified by diverse immunosuppressive regimens and by underlying host immune deficits. The impact of CMV infection on the transplant recipient reflects cellular changes and corresponding host responses, the convergence of which has been termed the "indirect effects" of CMV infection. Future studies will clarify interactions between CMV infection and allograft injury and will guide interventions that may enhance clinical outcomes in transplantation.

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Section: Genetics and Variability In Clinical Diseasementioning

confidence: 99%

The Cell Biology of Cytomegalovirus: Implications for Transplantation

Kaminski

Fishman

2016

American Journal of Transplantation

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“…Recently, next-generation sequencing (NGS) provides a robust tool for the acquisition of massive genomic information from a variety of specimens. 11,12 Using the NGS technology, the whole-genome sequencing of viruses, such as Schmallenberg virus, Dengue virus, enterovirus, and respiratory syncytial virus, has been completed. [13][14][15] This approach is cost effective and highly efficient for the recovery of viral genome sequences, taking advantage of the detection and characterization of viral genomes and viral metagenomics.…”

Section: Introductionmentioning

confidence: 99%

Sequence-Independent, Single-Primer Amplification Next-Generation Sequencing of Hantaan Virus Cell Culture–Based Isolates

Song

Kim

et al. 2017

The American Society of Tropical Medicine and Hygiene

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Abstract. Hantaan virus (HTNV), identified in the striped field mouse (Apodemus agrarius), belongs to the genus Hantavirus of the family Bunyaviridae and contains tripartite RNA genomes, small (S), medium (M), and large (L) segments. HTNV is a major causative for hemorrhagic fever with renal syndrome (HFRS) with fatality rates ranging from 1% to 15% in the Republic of Korea (ROK) and China. Defining of HTNV whole-genome sequences and isolation of the infectious particle play a critical role in the characterization and preventive and therapeutic strategies of hantavirus outbreaks. Next-generation sequencing (NGS) provides an advanced tool for massive genomic sequencing of viruses. However, the isolation of viral infectious particles is a huge obstacle to investigate and develop anti-virals for hantaviruses. Here, we report 12 HTNV isolates from lung tissues of the striped field mouse in the highly HFRS-endemic areas. Sequence-independent, single-primer amplification (SISPA) NGS was attempted to recover the genomic sequences of HTNV isolates. The nucleotide sequence of HTNV S, M, and L segments were covered up to 99.4-100%, 97.5-100%, and 95.6-99.8%, respectively, based on the full length of the prototype HTNV 76-118. The whole-genome sequencing of HTNV isolates was accomplished by additional reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification cDNA ends (RACE) PCR. In conclusion, this study will lead to the attempt and usage of SISPA NGS technologies to delineate the whole-genome sequence of hantaviruses, providing a new era of viral genomics for the surveillance, trace, and disease risk management of HFRS incidents.

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“…A number of issues need to be resolved before sequencing-based infection testing can be widely considered as a clinical tool (36), including the establishment of pathogen-specific thresholds to discriminate between colonization, infection, and disease. This approach, however, may be of immediate use in formulating hypotheses for the occurrence and source of an infection.…”

Section: Discussionmentioning

confidence: 99%