Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods

Qiu, Yuan; Chen, Jiming; Wang, Tong; Hou, Guangyu; Zhuang, Qingye; Wu, Run; Wang, Kaicheng

doi:10.1016/j.virusres.2017.05.003

Cited by 10 publications

(6 citation statements)

References 29 publications

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“…We also did not evaluate any targeted NGS methods, which are likely more effective when performing routine sequencing for particular viral pathogens (49). Nevertheless, this study complements previous research investigating the utility of Ion Torrent and Illumina platforms (8, 13, 17–19, 50–54). As more public health laboratories begin to implement NGS, these results provide important considerations in weighing the advantages and disadvantages of using a particular sequencing platform or library preparation kit for performing metagenomic sequencing of RNA viruses.…”

Section: Discussionsupporting

confidence: 75%

Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses

Marine¹,

Valladares

Castro

et al. 2019

Preprint

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28Next-generation sequencing is a powerful tool for virological surveillance. While 29 Illumina® and Ion Torrent® sequencing platforms are used extensively for generating 30 viral RNA genome sequences, there is limited data comparing different platforms. We 31 evaluated the Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5 platforms using a 32 panel of sixteen specimens containing picornaviruses and human caliciviruses 33 (noroviruses and sapoviruses). The specimens were processed, using combinations of 34 three library preparation and five sequencing kits, to assess the quality and 35 completeness of assembled viral genomes, and an estimation of cost per sample to 36 generate the data was calculated. The choice of library preparation kit and sequencing 37 platform was found to impact the breadth of genome coverage and accuracy of 38 consensus viral genomes. The Ion Torrent S5 outperformed the older Ion Torrent PGM 39 platform in data quality and cost, and generated the highest proportion of reads for 40 enterovirus D68 samples. However, indels at homopolymer regions impacted the 41 accuracy of consensus genome sequences. For lower throughput sequencing runs (i.e., 42 Ion Torrent 510 or Illumina MiSeq Nano V2), the cost per sample was lower on the 43 MiSeq platform, whereas with higher throughput runs (Ion Torrent 530 or Illumina MiSeq 44 V2) the cost per sample was comparable. These findings suggest that the Ion Torrent 45 S5 and Illumina MiSeq platforms are both viable options for genomic sequencing of 46 RNA viruses, each with specific advantages and tradeoffs.47 48Conventional Sanger sequencing has been the gold standard for genomic analysis of 49 pathogens in public health laboratories for over three decades. However, the expansion 50 of next-generation sequencing (NGS) technologies has increased demand for high-51 throughput sequencing of genomes at a lower cost (1). NGS has been used extensively 52 for routine surveillance and outbreak investigation of numerous viral RNA pathogens. 53The exponential growth of genomic information generated for important pathogens has 54 provided increased resolution for molecular epidemiology, as well as information 55 necessary for the design of clinical assays and therapeutics (2-5). NGS methods are 56 also useful for identifying pathogens in syndromes where etiologies often remain 57 unknown (e.g., encephalitis, febrile illness), complementing or even replacing current 58 diagnostic methods (2, 6, 7). 60Over the past several years, the suppliers of high-capacity short-read sequencers have 61 been reduced to two manufacturers: Illumina (sequencing-by-synthesis technology) and 62 Thermo Fisher Scientific (Ion Torrent semi-conductor sequencing technology) (3). 63 Illumina platforms have been used to generate nearly 90% of NGS data worldwide 64 (https://www.wired.com/2016/02/gene-sequencing-goliath-wants-get-bigger-still/). 65Illumina produces several benchtop and production-scale sequencers with data outputs 66 varying from 1.2 gigabases (Gb) to 6 terabases (Tb). In mic...

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Section: Discussionsupporting

confidence: 75%

Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses

Marine¹,

Valladares

Castro

et al. 2019

Preprint

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“…Fish-related viruses have been previously observed in domestic ducks [ 26 ], but the previous study did not mention families or species. Moreover, we identified 22 families that had not been previously detected in fecal samples of migratory wild ducks and 36 viral families that had been previously observed in other studies of fecal or cloacal samples of ducks [ 25 , 26 , 45 ]. Therefore, viruses relevant to veterinary medicine that are possibly disseminated by wild ducks should be monitored, and the possible role of wild ducks harboring human viruses should be further studied.…”

Section: Discussionmentioning

confidence: 89%

Fecal virome composition of migratory wild duck species

et al. 2018

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The fecal virome comprises a complex diversity of eukaryotic viruses, phages and viruses that infect the host. However, little is known about the intestinal community of viruses that is present in wild waterfowl, and the structure of this community in wild ducks has not yet been studied. The fecal virome compositions of six species of wild dabbling ducks and one species of wild diving duck were thus analyzed. Fecal samples were collected directly from the rectums of 60 ducks donated by hunters. DNA and RNA virus particles were purified and sequenced using the MiSeq Illumina platform. The reads obtained from the sequencing were analyzed and compared with sequences in the GenBank database. Viral-related sequences from the Herpesviridae, Alloherpesviridae, Adenoviridae, Retroviridae and Myoviridae viral families showed the highest overall abundances in the samples. The virome analysis identified viruses that had not been found in wild duck feces and revealed distinct virome profiles between different species and between samples of the same species. This study increases our understanding of viruses in wild ducks as possible viral reservoirs and provides a basis for further studying and monitoring the transmission of viruses from wild animals to humans and disease outbreaks in domestic animals.

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“…Sequencing libraries of the extracted viral RNA from the pooled samples from the six farms (Table 1) were constructed using the Ion Total RNA-Seq kit v2 with some modifications [10]. Briefly, the extracted viral RNA was quantified by Qubit assays (Life Technologies, USA) to ensure samples were greater than 100ng/μL and then digested using RNase III.…”

Section: Methodsmentioning

confidence: 99%

“…The use of NGS has been confirmed for detecting microorganisms in human clinical samples [6–8] and infectious viruses in numerous animal species. The method of preparing the sequencing libraries and the NGS platform used in this study have been evaluated previously [9, 10], and viruses in clinical samples from single animal hosts have also been detected using the same standard NGS procedure in our laboratory [10–12].…”

Section: Introductionmentioning

confidence: 99%

Viral infection detection using metagenomics technology in six poultry farms of eastern China

et al. 2019

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With rapidly increasing animal pathogen surveillance requirements, new technologies are needed for a comprehensive understanding of the roles of pathogens in the occurrence and development of animal diseases. We applied metagenomic technology to avian virus surveillance to study the main viruses infecting six poultry farms in two provinces in eastern China. Cloacal/throat double swabs were collected from 60 birds at each farm according to a random sampling method. The results showed that the method could simultaneously detect major viruses infecting farms, including avian influenza virus, infectious bronchitis virus, Newcastle disease virus, rotavirus G, duck hepatitis B virus, and avian leukemia virus subgroup J in several farms. The test results were consistent with the results from traditional polymerase chain reaction (PCR) or reverse transcription-PCR analyses. Five H9N2 and one H3N8 avian influenza viruses were detected at the farms and were identified as low pathogenic avian influenza viruses according to HA cleavage sites analysis. One detected Newcastle disease virus was classified as Class II genotype I and avirulent type according to F0 cleavage sites analysis. Three avian infectious bronchitis viruses were identified as 4/91, CK/CH/LSC/99I and TC07-2 genotypes by phylogenetic analysis of S1 genes. The viral infection surveillance method using metagenomics technology enables the monitoring of multiple viral infections, which allows the detection of main infectious viruses.

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Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods

Cited by 10 publications

References 29 publications

Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses

Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses

Fecal virome composition of migratory wild duck species

Viral infection detection using metagenomics technology in six poultry farms of eastern China

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