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. 2025 Apr:333:115109.
doi: 10.1016/j.jviromet.2025.115109. Epub 2025 Jan 16.

Rapid, inexpensive multiplex pathogen detection using resequencing microarrays

Kendall Hoff  1 , Xun Ding  2 , Xing Liang Liu  3 , Ju-Yu Lin  2 , John Duque  2 , Su Yu  2 , Samantha Dung  2 , Filip Crnogorac  2 , Glenn McGall  2 , Jie Duan  3 , John Chiang  3 , Jeremy Edwards  4 , Wei Zhou  2
Affiliations

Rapid, inexpensive multiplex pathogen detection using resequencing microarrays

Kendall Hoff et al. J Virol Methods. 2025 Apr.

Abstract

Humanity faces an ongoing battle at the microscopic level to identify, contain, and treat outbreaks of numerous pathogens each year. Global genomic surveillance is the first step in monitoring outbreaks, but high-throughput methods are expensive and time-consuming. To solve this problem, we designed and manufactured a resequencing microarray capable of identifying 35 viral pathogens, 21 pathogenic bacteria, 16 antibiotic resistance genes, and 6 controls. We then developed an assay using these microarrays for the rapid detection of SARS-CoV-2, influenza A, and influenza B. Here, we present the clinical validation data for this test. The assay requires less than two hours to complete and has high-sensitivity, with limits of detection of 125 copies per mL for SARS-CoV-2, 0.01-0.05 TCID50/mL for influenza A, and 0.005-0.01 TCID50/mL for influenza B. The microarrays used for these assays are easily mass-produced using wafer-scale synthesis, making this an affordable option for pathogen screening with broad implications in public health.

Keywords: COVID-19; DNA Chip; DNA Sequencing; RT-PCR; SARS-CoV-2; Tiling array; VPCR.

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Conflict of interest statement

Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Jeremy Edwards reports financial support was provided by Centrillion Technologies, Inc. Kendall Hoff, Xun Ding, John Duque, Su Yu, Samantha Dung, Filip Crnogorac, Glenn McGall, Wei Zhou reports financial support was provided by Centrillion Technologies, Inc. Xing Liang Liu, Ju-Yu Lin, Jie Duan, John Chiang reports financial support was provided by Molecular Vision Lab. Jeremy Edwards reports a relationship with Centrillion that includes: board membership, consulting or advisory, and equity or stocks. Kendall Hoff, Xun Ding, John Duque, Su Yu, Samantha Dung, Filip Crnogorac, Glenn McGall, Wei Zhou reports a relationship with Centrillion Technologies, Inc. that includes: employment and equity or stocks. Wei Zhou reports a relationship with Centrillion Technologies, Inc. that includes: board membership, employment, and equity or stocks. Xing Liang Liu, Ju-Yu Lin, Jie Duan, John Chiang reports a relationship with Molcular Vision Lab that includes: employment and equity or stocks. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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