Detection and Identification of Common Food-Borne Viruses with a Tiling Microarray

Chen, Haifeng; Mammel, Mark K.; Kulka, Mike; Patel, Isha R.; Jackson, Scott A.; Goswami, Biswendu B.

doi:10.2174/1874357901105010052

Cited by 19 publications

(15 citation statements)

References 23 publications

(38 reference statements)

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“…Several DNA microarrays have been previously reported for identification of the main known gastrointestinal pathogenic viruses (59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75); however, they were oriented mostly to the identification or subtyping of one viral species, and none had specifically addressed the list of viruses that can be found in stool samples.…”

Section: Discussionmentioning

confidence: 99%

DNA Microarray for Detection of Gastrointestinal Viruses

Martı́nez¹,

Río²,

Gutiérrez³

et al. 2015

J Clin Microbiol

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f Gastroenteritis is a clinical illness of humans and other animals that is characterized by vomiting and diarrhea and caused by a variety of pathogens, including viruses. An increasing number of viral species have been associated with gastroenteritis or have been found in stool samples as new molecular tools have been developed. In this work, a DNA microarray capable in theory of parallel detection of more than 100 viral species was developed and tested. Initial validation was done with 10 different virus species, and an additional 5 species were validated using clinical samples. Detection limits of 1 ؋ 10 3 virus particles of Human adenovirus C (HAdV), Human astrovirus (HAstV), and group A Rotavirus (RV-A) were established. Furthermore, when exogenous RNA was added, the limit for RV-A detection decreased by one log. In a small group of clinical samples from children with gastroenteritis (n ‫؍‬ 76), the microarray detected at least one viral species in 92% of the samples. Single infection was identified in 63 samples (83%), and coinfection with more than one virus was identified in 7 samples (9%). The most abundant virus species were RV-A (58%), followed by Anellovirus (15.8%), HAstV (6.6%), HAdV (5.3%), Norwalk virus (6.6%), Human enterovirus (HEV) (9.2%), Human parechovirus (1.3%), Sapporo virus (1.3%), and Human bocavirus (1.3%). To further test the specificity and sensitivity of the microarray, the results were verified by reverse transcription-PCR (RT-PCR) detection of 5 gastrointestinal viruses. The RT-PCR assay detected a virus in 59 samples (78%). The microarray showed good performance for detection of RV-A, HAstV, and calicivirus, while the sensitivity for HAdV and HEV was low. Furthermore, some discrepancies in detection of mixed infections were observed and were addressed by reverse transcription-quantitative PCR (RT-qPCR) of the viruses involved. It was observed that differences in the amount of genetic material favored the detection of the most abundant virus. The microarray described in this work should help in understanding the etiology of gastroenteritis in humans and animals.

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Section: Discussionmentioning

confidence: 99%

DNA Microarray for Detection of Gastrointestinal Viruses

Martı́nez¹,

Río²,

Gutiérrez³

et al. 2015

J Clin Microbiol

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“…Virus detection and genotyping were assessed using the FDA_EVIR microarray chips described in previous study (Chen et al 2011 ). The microarray, which was customer ordered to be manufactured by Affymetrix Inc (Affymetrix, Santa Clara, CA), interrogates approximately 91,000 25-mer oligonucleotide probes that derive from genomes of major human enteric viruses including NoV, HAV, CXKV, rotavirus, sapovirus, astrovirus, hepatitis E virus, and adenovirus.…”

Section: Methodsmentioning

confidence: 99%

“…The microarray chips were scanned with GeneChip ® scanner (Affymetrix). The primary microarray data were analyzed with a script based on Affymetrix power tools as described previously (Chen et al 2011 ). The results were considered positive for virus detection when the normalized hybridization signal intensities from the virus-specific array elements were three times greater than the background signal intensity.…”

Section: Methodsmentioning

confidence: 99%

Sequence-independent amplification coupled with DNA microarray analysis for detection and genotyping of noroviruses

Yan

Mammel

et al. 2015

AMB Expr

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Noroviruses (NoVs) have high levels of genetic sequence diversities, which lead to difficulties in designing robust universal primers to efficiently amplify specific viral genomes for molecular analysis. We here described the practicality of sequence-independent amplification combined with DNA microarray analysis for simultaneous detection and genotyping of human NoVs in fecal specimens. We showed that single primer isothermal linear amplification (Ribo-SPIA) of genogroup I (GI) and genogroup II (GII) NoVs could be run through the same amplification protocol without the need to design and use any virus-specific primers. Related virus could be subtyped by the unique pattern of hybridization with the amplified product to the microarray. By testing 22 clinical fecal specimens obtained from acute gastroenteritis cases as blinded samples, 2 were GI positive and 18 were GII positive as well as 2 negative for NoVs. A NoV GII positive specimen was also identified as having co-occurrence of hepatitis A virus. The study showed that there was 100 % concordance for positive NoV detection at genogroup level between the results of Ribo-SPIA/microarray and the phylogenetic analysis of viral sequences of the capsid gene. In addition, 85 % genotype agreement was observed for the new assay compared to the results of phylogenetic analysis.

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“…In recent years, a variety of molecular approaches, such as microarray, multiplexing amplifications and nested amplification other than real-time PCR, have been developed. Several groups have developed microarrays for simultaneous detection, characterisation and separation of NoV and HAV (3,10). However, the sensitivity of multiplex methods is often low (36).…”

Section: Recent Advances In Foodborne Virus Detectionmentioning

confidence: 99%

Development of improved analytical methods for use in animal health and in foodborne disease surveillance for source attribution

Widén

Leijon

Engvall

et al. 2013

Rev. Sci. Tech. OIE

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Considering the 'One Health' principles, the links between animal and human health are very strong. Both domestic and wild animals are sources of infectious agents that cause diseases in humans. Poor animal health may also indirectly affect human health, through reduced access to food. A large number of infectious diseases of animals, the transboundary animal diseases, spread rapidly across borders. Robust and accurate diagnostic assays are needed to detect the infectious agents rapidly and to limit their spread. A large arsenal of novel assays has been developed during the last three decades, with a tremendous impact on the detection of infectious agents. The new diagnostic methods are mostly laboratory-based and expensive, requiring sophisticated equipment and special skills. However, rapid and cheap field-based assays have also been developed. Herein, the authors give several examples of the development of novel assays, with special focus on the 'One Health' principles.

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Detection and Identification of Common Food-Borne Viruses with a Tiling Microarray

Cited by 19 publications

References 23 publications

DNA Microarray for Detection of Gastrointestinal Viruses

DNA Microarray for Detection of Gastrointestinal Viruses

Sequence-independent amplification coupled with DNA microarray analysis for detection and genotyping of noroviruses

Development of improved analytical methods for use in animal health and in foodborne disease surveillance for source attribution

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