Highly Accurate Chip-Based Resequencing of SARS-CoV-2 Clinical Samples

Authors

• Kendall Hoff, Centrillion Technologies, Palo Alto, California 94303, United States
• Xun Ding, Centrillion Technologies, Palo Alto, California 94303, United States
• Lucas Carter, Centrillion Technologies, Palo Alto, California 94303, United States
• John Duque, Centrillion Technologies, Palo Alto, California 94303, United States
• Ju-Yu Lin, Centrillion Technologies, Palo Alto, California 94303, United States
• Samantha Dung, Centrillion Technologies, Palo Alto, California 94303, United States
• Priyanka Singh, Centrillion Technologies, Palo Alto, California 94303, United States
• Jiayi Sun, Centrillion Technologies, Palo Alto, California 94303, United States
• Filip Crnogorac, Centrillion Technologies, Palo Alto, California 94303, United States
• Radha Swaminathan, Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
• Emily N. Alden, Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
• Xuechen Zhu, Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
• Ryota Shimada, Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
• Marijan Posavi, Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
• Noah Hull, Wyoming Public Health Laboratory, Wyoming Department of Health, Cheyenne, Wyoming 82007, United States
• Darrell L. Dinwiddie, Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, United States
• Adam M. Halasz, Department of Mathematics, West Virginia University, Morgantown, West Virginia 26506, United States
• Glenn McGall, Centrillion Technologies, Palo Alto, California 94303, United States
• Wei Zhou, Centrillion Technologies, Palo Alto, California 94303, United States
• Jeremy S. Edwards, Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States

Document Type

Article

Publication Date

4-27-2021

Abstract

SARS-CoV-2 has infected over 128 million people worldwide, and until a vaccine is developed and widely disseminated, vigilant testing and contact tracing are the most effective ways to slow the spread of COVID-19. Typical clinical testing only confirms the presence or absence of the virus, but rather, a simple and rapid testing procedure that sequences the entire genome would be impactful and allow for tracing the spread of the virus and variants, as well as the appearance of new variants. However, traditional short read sequencing methods are time consuming and expensive. Herein, we describe a tiled genome array that we developed for rapid and inexpensive full viral genome resequencing, and we have applied our SARS-CoV-2-specific genome tiling array to rapidly and accurately resequence the viral genome from eight clinical samples. We have resequenced eight samples acquired from patients in Wyoming that tested positive for SARS-CoV-2. We were ultimately able to sequence over 95% of the genome of each sample with greater than 99.9% average accuracy.

Publication Title

Langmuir : the ACS journal of surfaces and colloids

ISSN

1520-5827

Volume

37

Issue

16

First Page

4763

Last Page

4771

DOI

10.1021/acs.langmuir.0c02927

Recommended Citation

Hoff K, Ding X, Carter L, Duque J, Lin JY, Dung S, Singh P, Sun J, Crnogorac F, Swaminathan R, Alden EN, Zhu X, Shimada R, Posavi M, Hull N, Dinwiddie D, Halasz AM, McGall G, Zhou W, Edwards JS. Highly Accurate Chip-Based Resequencing of SARS-CoV-2 Clinical Samples. Langmuir. 2021 Apr 27;37(16):4763-4771. doi: 10.1021/acs.langmuir.0c02927. Epub 2021 Apr 13. PMID: 33848173; PMCID: PMC8056606.