Application of next generation sequencing toward sensitive detection of enteric viruses isolated from celery samples as an example of produce

Yang, Zhihui; Mammel, Mark K.; Papafragkou, Efstathia; Hida, Kaoru; Elkins, Christopher A.; Kulka, Michael

doi:10.1016/j.ijfoodmicro.2017.07.021

Cited by 32 publications

(43 citation statements)

References 44 publications

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“…This observation has already been reported by others, as well as our group [ 22 , 31 , 32 ], and it has been explained by the inherent difficulty in recovering readable sequences at the ends of DNA fragments from the short sequences produced by Illumina. Consistent with our previous observations and other reports, samples with higher load had better coverage [ 22 , 33 ].…”

Section: Resultssupporting

confidence: 93%

See 1 more Smart Citation

Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique

Petronella

Ronholm

Suresh³

et al. 2018

BMC Infect Dis

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BackgroundHuman norovirus is the leading cause of viral gastroenteritis globally, and the GII.4 has been the most predominant genotype for decades. This genotype has numerous variants that have caused repeated epidemics worldwide. However, the molecular evolutionary signatures among the GII.4 variants have not been elucidated throughout the viral genome.MethodA metagenomic, next-generation sequencing method, based on Illumina RNA-Seq, was applied to determine norovirus sequences from clinical samples.ResultsHerein, the obtained deep-sequencing data was employed to analyze full-genomic sequences from GII.4 variants prevailing in Canada from 2012 to 2016. Phylogenetic analysis demonstrated that the majority of these sequences belong to New Orleans 2009 and Sydney 2012 strains, and a recombinant sequence was also identified. Genome-wide similarity analyses implied that while the capsid gene is highly diverse among the isolates, the viral protease and polymerase genes remain relatively conserved. Numerous amino acid substitutions were observed at each putative antigenic epitope of the VP1 protein, whereas few amino acid changes were identified in the polymerase protein. Co-infection with other enteric RNA viruses was investigated and the astrovirus genome was identified in one of the samples.ConclusionsOverall this study demonstrated the application of whole genome sequencing as an important tool in molecular characterization of noroviruses.Electronic supplementary materialThe online version of this article (10.1186/s12879-018-3419-8) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 93%

“…Genetic recombination is a major driving force in the evolution and emergence of novel GII.4 variants [ 11 , 12 , 33 , 35 ]. Genetic recombination occurs when a single cell is co-infected with two NoV variants and, therefore, indicates co-infection of an individual with both variants.…”

Section: Resultsmentioning

confidence: 99%

Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique

Petronella

Ronholm

Suresh³

et al. 2018

BMC Infect Dis

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“…The very novel analytical methods applied to detect and characterize HAV in food and environmental samples rely on next generation sequencing (NGS) techniques. The wide potential of NGS includes the characterization of viral quasispecies heterogeneity (Yang et al 2018) and the metagenomics approach represent a promising solution for detecting all viruses (virome), delivering genomic information and discovering unknown viruses (Nieuwenhuijse and Koopmans 2017;Yang et al 2017). NGS have been successfully applied for amplification-independent detection of norovirus and HAV spiked in celery samples at low copy using both targeted and metagenomics approaches (Yang et al 2017).…”

Section: Hav Detection In Foodmentioning

confidence: 99%

Hepatitis A infections from food

Randazzo

Sánchez

2020

J. Appl. Microbiol.

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Food contaminated by hepatitis A virus (HAV) is responsible of the 2-7% of all HAV outbreaks worldwide. This review provides a description of the HAV characteristics, its infectivity and epidemiological features. In addition, this review compiles existing original papers reporting HAV prevalence, viral titres in foodstuffs and the risk associated with food contamination. The purpose of this revision is to conduct a structured and systematic review of the published molecular procedures for HAV detection in food, including the assessment of its infectivity. based on the analysis of a 168-nucleotide segment of the VP1-2A region, HAV is classified in six genotypes. Genotypes I, II and III, have human origin and are divided into subtypes A and B, while genotypes IV, V and VI cause infections in simians (Desbois et al. 2010). Features of HAV infection The course of hepatitis A ranges from mild to severe, and is typically more severe in adults than in children (<6 years), that are often asymptomatic. Common symptoms associated with acute HAV infection are loss of appetite, fever, headache, nausea, diarrhoea, abdominal discomfort, anorexia, myalgia, dark-coloured urine and jaundice. HAV infection develops a lifelong immunity and does not result in chronic infection or chronic liver disease (Lemon et al. 2017). Adults with hepatitis A illness usually develop symptoms after a long incubation period of 14-28 days (up to 50 days) after the exposure, and a high numbers of virus particles are excreted reaching the maximum of up to 10 11 genome copies (gc) per gram of faeces just before the onset of symptoms. The fatality rate in HAV infections is lower than 0Á1%, although in elderly it may rise up to 1Á8-5Á4% (1Á8-5Á4%) (Bosch et al. 2016). Routes of transmission and epidemiology HAV is excreted in faeces and the main route of transmission is from person to person by the faecal-oral route

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“…To determine the HAV genome copy numbers in the samples, one-step RT-qPCR was carried out following the protocol previously published [1,24]. In brief, all RNA samples were analyzed in replicates using QuantiTect Probe RT-PCR kit (Qiagen) with a 25 µL reaction volume containing 5 µL RNA.…”

Section: Sample Preparation Rna Isolation and Viral Rna Quantificatimentioning

confidence: 99%

“…Double stranded cDNA libraries were generated from all the RNA samples above using a TruSeq stranded mRNA prep kit (Illumina) following our previously published protocol [1,24]. The total RNA input of each F4-C1 sample ranged from 1 -3 µg.…”

Section: Library Generation and Sequencingmentioning

confidence: 99%

Inter- and Intra-Host Nucleotide Variations in Hepatitis A Virus in Culture and Clinical Samples Detected by Next-Generation Sequencing<strong> </strong>

Yang¹,

Mammel²,

Whitehouse³

et al. 2018

Preprint

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The accurate virus detection, strain discrimination, and source attribution of contaminated food items remains a persistent challenge because of the high mutation rates anticipated to occur in foodborne RNA viruses, such as Hepatitis A virus (HAV). This has led to predictions of the existence of more than one sequence variant between the hosts (inter-host) or within an individual host (intra-host). However, there have been no reports of intra-host variants from an infected single individual, and little is known about the accuracy of the single nucleotide variations (SNVs) calling with various methods. In this study, the presence and identity of viral SNVs, either between HAV clinical specimens or among a series of samples derived from HAV clone1-infected FRhK4 cells, were determined following analyses of nucleotide sequences generated using next-generation sequencing (NGS) and pyrosequencing methods. The results demonstrate the co-existence of inter- and intra-host variants both in the clinical specimens and the cultured samples. The discovery and confirmation of multi-viral RNAs in an infected individual is dependent on the strain discrimination at the SNV level, and critical for successful outbreak traceback and source attribution investigations. The detection of SNVs in a time series of HAV infected FRhK4 cells improved our understanding on the mutation dynamics determined probably by different selective pressures. Additionally, it demonstrated that NGS could potentially provide a valuable investigative approach toward SNV detection and identification for other RNA viruses.

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Application of next generation sequencing toward sensitive detection of enteric viruses isolated from celery samples as an example of produce

Cited by 32 publications

References 44 publications

Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique

Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique

Hepatitis A infections from food

Inter- and Intra-Host Nucleotide Variations in Hepatitis A Virus in Culture and Clinical Samples Detected by Next-Generation Sequencing<strong> </strong>

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