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SARS-CoV-2 Variant Identification Using a Genome Tiling Array and Genotyping Probes

View ORCID ProfileRyota Shimada, View ORCID ProfileEmily N. Alden, Kendall Hoff, Xun Ding, Jiayi Sun, Adam M. Halasz, Wei Zhou, View ORCID ProfileJeremy S. Edwards
doi: https://doi.org/10.1101/2021.05.11.443659
Ryota Shimada
1Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
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Emily N. Alden
1Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
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Kendall Hoff
2Centrillion Technologies, Palo Alto, CA 94303
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Xun Ding
2Centrillion Technologies, Palo Alto, CA 94303
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Jiayi Sun
2Centrillion Technologies, Palo Alto, CA 94303
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Adam M. Halasz
3Department of Mathematics, West Virginia University, Morgantown, WV, 26506
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Wei Zhou
2Centrillion Technologies, Palo Alto, CA 94303
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  • For correspondence: jsedward@unm.edu wzhou@centrilliontech.com
Jeremy S. Edwards
1Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
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  • For correspondence: jsedward@unm.edu wzhou@centrilliontech.com
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ABSTRACT

With over three million deaths worldwide attributed to the respiratory disease COVID-19 caused by the novel coronavirus SARS-CoV-2, it is essential that continued efforts be made to track the evolution and spread of the virus globally. We previously presented a rapid and cost-effective method to sequence the entire SARS-CoV-2 genome with 95% coverage and 99.9% accuracy. This method is advantageous for identifying and tracking variants in the SARS-CoV-2 genome when compared to traditional short read sequencing methods which can be time consuming and costly. Herein we present the addition of genotyping probes to our DNA chip which target known SARS-CoV-2 variants. The incorporation of the genotyping probe sets along with the advent of a moving average filter have improved our sequencing coverage and accuracy of the SARS-CoV-2 genome.

Competing Interest Statement

The authors declare the following competing financial interest(s): The Centrillion affiliated authors are employees and the company may commercialize the work described herein.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 11, 2021.
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SARS-CoV-2 Variant Identification Using a Genome Tiling Array and Genotyping Probes
Ryota Shimada, Emily N. Alden, Kendall Hoff, Xun Ding, Jiayi Sun, Adam M. Halasz, Wei Zhou, Jeremy S. Edwards
bioRxiv 2021.05.11.443659; doi: https://doi.org/10.1101/2021.05.11.443659
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SARS-CoV-2 Variant Identification Using a Genome Tiling Array and Genotyping Probes
Ryota Shimada, Emily N. Alden, Kendall Hoff, Xun Ding, Jiayi Sun, Adam M. Halasz, Wei Zhou, Jeremy S. Edwards
bioRxiv 2021.05.11.443659; doi: https://doi.org/10.1101/2021.05.11.443659

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