SARS-CoV-2 variant identification using a genome tiling array and genotyping probes.

With over 5.5 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. The authors 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 compared with traditional short-read sequencing methods which can be time-consuming and costly. Herein, the addition of genotyping probes to a DNA chip that targets known SARS-CoV-2 variants is presented. The incorporation of genotyping probe sets along with the advent of a moving average filter improved the sequencing coverage and accuracy of the SARS-CoV-2 genome.

Throughout the COVID-19 pandemic the virus known as SARS-CoV-2 has continued to mutate and evolve. It is imperative to continue to track these mutations and where the virus has traveled to best inform healthcare practices and global strategies to combat the virus. The authors previously developed a method to investigate 95% of this viral genome with 99.9% accuracy that was more cost-effective and less time-consuming than previous methods. In this work, specific markers were added to the technology to allow tracking of mutations in the virus that have already been documented. In doing so, the accuracy and how much of the viral genome can be sequenced was improved.

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

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.