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DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Using a Pan-Viral Microarray Assay Virochip to Screen Clinical Samples for Viral Pathogens

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Published on: April 27, 2011

Detecting SARS-CoV-2 and its variant strains with a full genome tiling array.

Limin Jiang¹, Yan Guo², Hui Yu²

¹University of New Mexico, Albuquerque, NM 87131, USA.

Briefings in Bioinformatics

|June 7, 2021

Summary

This summary is machine-generated.

A novel SARS-CoV-2 tiling array offers accurate, whole-genome detection of the virus and its variants. This cost-effective tool aids in rapid diagnosis and tracking mutations for pandemic control.

Keywords:

COVID-19 SARS-CoV-2 tiling array

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Area of Science:

Virology and Molecular Diagnostics
Genomics and Bioinformatics

Background:

The Coronavirus disease 2019 (COVID-19) pandemic necessitates rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants.
Current diagnostic methods often target limited genomic regions, leading to lower specificity and potential failure in identifying emerging SARS-CoV-2 variants.

Purpose of the Study:

To develop and validate the first SARS-CoV-2 tiling array for comprehensive, single-nucleotide resolution interrogation of the entire viral genome.
To establish a robust bioinformatics pipeline for analyzing tiling array data.
To demonstrate the array's utility in identifying key SARS-CoV-2 mutations and variants.

Main Methods:

Development of a SARS-CoV-2 tiling array covering the complete viral genome at single nucleotide resolution.
Creation of a bioinformatics protocol involving two base-calling methods for data analysis.
Validation of the tiling array by genotyping eight SARS-CoV-2 samples and comparing results against high-throughput sequencing.

Main Results:

The SARS-CoV-2 tiling array achieved a genome-wide accuracy of at least 99.5% compared to high-throughput sequencing.
Identification of the D614G mutation in the spike protein in 50% of samples, indicating early widespread distribution in the US.
Discovery of two novel nonsynonymous mutations (P13L, S197L) in the nucleocapsid protein of one sample.

Conclusions:

The developed SARS-CoV-2 tiling array provides a highly accurate, cost-effective ($5 per array), and rapid method for whole-genome sequencing and mutation detection.
This toolkit is invaluable for combating current and future viral pandemics through enhanced surveillance and diagnostic capabilities.
The array is currently being utilized for SARS-CoV-2 diagnosis by a CLIA-certified laboratory.