Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics

Zhao, Jiangqin; Liu, Jikun; Vemula, Sai V.; Lin, Corinna; Tan, Jiying; Ragupathy, Viswanath; Wang, Handong; Mbondji-Wonje, Christelle; Ye, Zhiping; Landry, Marie L.; Hewlett, Indira

doi:10.1371/journal.pone.0163175

Cited by 24 publications

(27 citation statements)

References 46 publications

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“…Due to multiple limitations including reliable access to specific pathogen-free ECEs in other countries, increasing importation costs, and regulatory restrictions that prevent rapid sample evaluation, we sought to improve virus characterization by performing NGS directly from swab samples. Although NGS has been previously used to characterize IAV from original samples (Ren et al, 2013;Seong et al, 2016;Wang et al, 2008;Zhao et al, 2016), such studies were not aimed at comparing it to viral isolation or determining whether it could result in different consensus sequences. Using swabs collected from wild birds in Guatemala during the 2013-2014 season, we amplified and obtained sequence information by swab-NGS from 29 out of 74 IAV rRT-PCR-positive samples.…”

Section: Discussionmentioning

confidence: 99%

“…The utility of next-generation sequencing (NGS) and the ability to sequence directly from the original swab material for rapid IAV detection will produce more complete and accurate data reflective of naturally occurring subtypes and genetic diversity (McGinnis, Laplante, Shudt, & George, 2016;Zhao et al, 2016). In the present report, we show how performing NGS from original swab (swab-NGS) material can improve IAV characterization from field samples.…”

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confidence: 88%

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Improved detection of influenza A virus from blue‐winged teals by sequencing directly from swab material

Ferreri

Ortiz

Geiger

et al. 2019

Ecology and Evolution

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The greatest diversity of influenza A virus (IAV) is found in wild aquatic birds of the orders Anseriformes and Charadriiformes. In these birds, IAV replication occurs mostly in the intestinal tract. Fecal, cloacal, and/or tracheal swabs are typically collected and tested by real‐time RT‐PCR (rRT‐PCR) and/or by virus isolation in embryonated chicken eggs in order to determine the presence of IAV. Virus isolation may impose bottlenecks that select variant populations that are different from those circulating in nature, and such bottlenecks may result in artifactual representation of subtype diversity and/or underrepresented mixed infections. The advent of next‐generation sequencing (NGS) technologies provides an opportunity to explore to what extent IAV subtype diversity is affected by virus isolation in eggs. In the present work, we evaluated the advantage of sequencing by NGS directly from swab material of IAV rRT‐PCR‐positive swabs collected during the 2013–14 surveillance season in Guatemala and compared to results from NGS after virus isolation. The results highlight the benefit of sequencing IAV genomes directly from swabs to better understand subtype diversity and detection of alternative amino acid motifs that could otherwise escape detection using traditional methods of virus isolation. In addition, NGS sequencing data from swabs revealed reduced presence of defective interfering particles compared to virus isolates. We propose an alternative workflow in which original swab samples positive for IAV by rRT‐PCR are first subjected to NGS before attempting viral isolation. This approach should speed the processing of samples and better capture natural IAV diversity. OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.3h2n106.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 88%

Improved detection of influenza A virus from blue‐winged teals by sequencing directly from swab material

Ferreri

Ortiz

Geiger

et al. 2019

Ecology and Evolution

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“…The additional benefit of sequencing over virus isolation is that the sequences would be useful for analyzing the influenza virus outbreak clusters [338], virus evolution or reassortment [339] using phylogenetic analyses in different gene segments. A recent study reported that next-generation sequencing can be useful in the influenza virus diagnosis and for the identification of the novel virulence markers and drug resistance [340].…”

Section: Discussionmentioning

confidence: 99%

A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide

Chauhan

Gordon

2020

Pathogens

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The global anxiety and a significant threat to public health due to the current COVID-19 pandemic reiterate the need for active surveillance for the zoonotic virus diseases of pandemic potential. Influenza virus due to its wide host range and zoonotic potential poses such a significant threat to public health. Swine serve as a "mixing vessel" for influenza virus reassortment and evolution which as a result may facilitate the emergence of new strains or subtypes of zoonotic potential. In this context, the currently available scientific data hold a high significance to unravel influenza virus epidemiology and evolution. With this objective, the current systematic review summarizes the original research articles and case reports of all the four types of influenza viruses reported in swine populations worldwide. A total of 281 articles were found eligible through screening of PubMed and Google Scholar databases and hence were included in this systematic review. The highest number of research articles (n = 107) were reported from Asia, followed by Americas (n = 97), Europe (n = 55), Africa (n = 18),

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“…Other techniques, such as gDNA depletion and host RNA depletion to enrich for viral RNA [13] and DNase pretreatment of the allantoic fluid to enrich for viral particles, have also been described [14]. Different methods have been employed for producing cDNA following enrichment, including sequence-independent single primer amplification (SISPA) and universal primers which have been used for sequencing RNA viruses [4, 15] including Newcastle disease virus (NDV) [11] and avian paramyxovirus (APMV) 4 and 6 [16]. …”

Section: Introductionmentioning

confidence: 99%

A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

Dimitrov

Sharma

Volkening

et al. 2017

Virol J

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BackgroundNext-generation sequencing (NGS) allows ultra-deep sequencing of nucleic acids. The use of sequence-independent amplification of viral nucleic acids without utilization of target-specific primers provides advantages over traditional sequencing methods and allows detection of unsuspected variants and co-infecting agents. However, NGS is not widely used for small RNA viruses because of incorrectly perceived cost estimates and inefficient utilization of freely available bioinformatics tools.MethodsIn this study, we have utilized NGS-based random sequencing of total RNA combined with barcode multiplexing of libraries to quickly, effectively and simultaneously characterize the genomic sequences of multiple avian paramyxoviruses. Thirty libraries were prepared from diagnostic samples amplified in allantoic fluids and their total RNAs were sequenced in a single flow cell on an Illumina MiSeq instrument. After digital normalization, data were assembled using the MIRA assembler within a customized workflow on the Galaxy platform.ResultsTwenty-eight avian paramyxovirus 1 (APMV-1), one APMV-13, four avian influenza and two infectious bronchitis virus complete or nearly complete genome sequences were obtained from the single run. The 29 avian paramyxovirus genomes displayed 99.6% mean coverage based on bases with Phred quality scores of 30 or more. The lower and upper quartiles of sample median depth per position for those 29 samples were 2984 and 6894, respectively, indicating coverage across samples sufficient for deep variant analysis. Sample processing and library preparation took approximately 25–30 h, the sequencing run took 39 h, and processing through the Galaxy workflow took approximately 2–3 h. The cost of all steps, excluding labor, was estimated to be 106 USD per sample.ConclusionsThis work describes an efficient multiplexing NGS approach, a detailed analysis workflow, and customized tools for the characterization of the genomes of RNA viruses. The combination of multiplexing NGS technology with the Galaxy workflow platform resulted in a fast, user-friendly, and cost-efficient protocol for the simultaneous characterization of multiple full-length viral genomes. Twenty-nine full-length or near-full-length APMV genomes with a high median depth were successfully sequenced out of 30 samples. The applied de novo assembly approach also allowed identification of mixed viral populations in some of the samples.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-017-0741-5) contains supplementary material, which is available to authorized users.

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Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics

Cited by 24 publications

References 46 publications

Improved detection of influenza A virus from blue‐winged teals by sequencing directly from swab material

Improved detection of influenza A virus from blue‐winged teals by sequencing directly from swab material

A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide

A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

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