Viral diagnosis in Indian livestock using customized microarray chips

Yadav, Brijesh Singh; Pokhriyal, Mayank; Ratta, Barkha; Kumar, Ajay; Saxena, M.; Sharma, Bhaskar

doi:10.6026/97320630011489

Cited by 4 publications

(5 citation statements)

References 18 publications

(28 reference statements)

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“…The DNA microarray platform is suitable for multiplex detection of many targets in a single sample and has been widely used for multiplex pathogen detection (Kostrzynska and Bachand, 2006;Yadav et al, 2015). Conventional microarray requires a substantial amount of manual processing, multiple pieces of equipment for array preparation, and longer time for passive target-probe hybridization.…”

Section: Introductionmentioning

confidence: 99%

A novel multiplex PCR-electronic microarray assay for rapid and simultaneous detection of bovine respiratory and enteric pathogens

Thanthrige-Don

Lung

Furukawa-Stoffer

et al. 2018

Journal of Virological Methods

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Respiratory and enteric diseases continue to be two major causes of economic losses to the cattle industry worldwide. Despite their multifactorial etiology, the currently available diagnostic tests for bovine respiratory disease complex (BRDC) and bovine enteric disease (BED) are single-pathogen-tests. DNA microarray when combined with multiplex polymerase chain reaction (PCR) is a powerful tool in detection and differentiation of multiple pathogens in a single sample. This study reports development and initial validation of two independent highly sensitive and specific multiplex PCR-electronic microarray assays, one for the detection and differentiation of pathogens of the BRDC and the other for detection and differentiation of pathogens of the BED. The BRDC multiplex PCR-microarray assay was able to detect and differentiate four bacteria (Mannheimia haemolytica, Histophilus somni, Pasteurella multocida, and Mycoplasma bovis) and five viruses [bovine parainfluenza virus-3, bovine respiratory syncytial virus, bovine herpesvirus-1, bovine coronavirus (BCoV), and bovine viral diarrhea virus (BVDV)] associated with BRDC. The BED multiplex PCR- microarray- assay was able to detect and differentiate four bacteria (Clostridium perfringens, Escherichia coli, Salmonella enterica Dublin, and Salmonella enterica Typhimurium), three protozoa (Eimeria zuernii, Eimeria bovis, and Cryptosporidium parvum), and four viruses (bovine torovirus, bovine rotavirus, BCoV, and BVDV) associated with the BED. Both assays detected their respective targets individually or in combination when present. The limit-of-detection of each assay at the PCR amplification and DNA microarray levels was determined using previously titrated laboratory amplified target pathogens or using quantified synthetic nucleotides. Both assays showed very high analytical sensitivity and specificity, and were validated using a limited number of clinical samples. The BRDC and BED multiplex PCR- microarray-assays developed in this study, with further clinical validation, could be used in veterinary diagnostic laboratories for the rapid and simultaneous identification of pathogens to facilitate quick and accurate decision making for the control and treatment of these two economically important disease complexes. Furthermore, these assays could be very effective tools in epidemiological studies as well as for screening of healthy animals to identify carriers that may potentially develop BRDC or BED.

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Section: Introductionmentioning

confidence: 99%

A novel multiplex PCR-electronic microarray assay for rapid and simultaneous detection of bovine respiratory and enteric pathogens

Thanthrige-Don

Lung

Furukawa-Stoffer

et al. 2018

Journal of Virological Methods

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“…First broad range chip was used for FMD virus identification (Baxiet al,2006). Pan viral DNA microarray are available for identification of Orbivirus (Gardneret al,2013).Animal viruses like FMDV, Vesicular stomatitis virus, swine vesicular disease virus, BHV-1, BVDV1, VESV (causing vesicular lesions in livestock species) and Enterovirus (Nishizukaet al,2003;Nandi and Chauhan,2006), were detected by using long oligonucleotide microarray technique.Recently, a team of scientists developed a microarray chip for livestock virus diagnosis at IVRI, India (Yadav et al,2015). This chip was used for detection of first case of New Castle Disease Virusin sheep (i.e.…”

Section: Parasitic Diseasesmentioning

confidence: 99%

Molecular Pathology: An Advanced Approach for Rapid Diagnosis of Diseases

Harit¹,

Chauhan²

2020

IJAR

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“…The capability of microarray to detect a large number of genes was used for diagnosis at the beginning of this century when the SARS corona virus was identified using a diagnostic microarray chip (Wang et al 2002). Since then several microarray chips have been developed and tested (Wang et al 2002(Wang et al , 2003Martín et al 2006;Chiu et al 2006;Quan et al 2007;Gardner et al 2010;Yadav et al 2015).…”

Section: Viral Diseases In Humans and Livestockmentioning

confidence: 99%

“…The virus identification from the signal intensity data makes use of different approaches. The simplest approach for predicting presence of virus in the sample is based on averaging signal intensity of all the probes of a virus or virus genus/family: if it is above a cutoff value, virus is predicted to be present; the other approach is based on the number/percentage of probes giving positive signal above a preset threshold (Sharma et al 2012;Yadav et al 2015). The first broad-spectrum virusdetecting microarray chip, ViroChip, made prediction based on the aggregate hybridization pattern (Wang et al 2003).…”

Section: Data Processing On the Basis Of Signal Intensitymentioning

confidence: 99%

Bioinformatics and Microarray-Based Technologies to Viral Genome Sequence Analysis

Pokhriyal

Ratta

Yadav

2019

Microbial Genomics in Sustainable Agroecosystems

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Identification of microbial pathogen is an important event which lead to diagnosis, treatment, and control of infections produce by them. The high-throughput technology like microarray and new-generation sequencing machine are able to generate huge amount of nucleotide sequences of viral and bacterial genome of both known and unknown pathogens. Few years ago it was the DNA microarrays which had great potential to screen all the known pathogens and yet to be identified pathogen simultaneously. But after the development of a new generation sequencing, technologies and advance computational approach researchers are looking forward for a complete understanding of microbes and host interactions. The powerful sequencing platform is rapidly transforming the landscape of microbial identification and characterization. As bioinformatics analysis tools and databases are easily available to researchers, the enormous amount of data generated can be meaningfully handled for better understanding of the microbial world. Here in this chapter, we present commentary on how the computational method incorporated with sequencing technique made easy for microbial detection and characterization.

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Viral diagnosis in Indian livestock using customized microarray chips

Cited by 4 publications

References 18 publications

A novel multiplex PCR-electronic microarray assay for rapid and simultaneous detection of bovine respiratory and enteric pathogens

A novel multiplex PCR-electronic microarray assay for rapid and simultaneous detection of bovine respiratory and enteric pathogens

Molecular Pathology: An Advanced Approach for Rapid Diagnosis of Diseases

Bioinformatics and Microarray-Based Technologies to Viral Genome Sequence Analysis

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