Identifying and Tracing Variant Strains of SARS-CoV-2 in Large Populations with Pangenome Analysis

Enabled by plexWell™ Library Prep Technology

Stanford University

In the past year, the propensity for mutation in the genome of the SARS-CoV-2 virus has led to the emergence of different strains around the globe, putting the onus on researchers to quickly identify and accurately trace transmission patterns of these variant strains. Unfortunately, the use of traditional molecular linkage research methods, such as conventional sequence alignment, proved to be too slow and inefficient when analyzing thousands of viral samples obtained in clinical settings from patients around the world.

In order to help trace and control the spread of the coronavirus and its emerging variants, researchers from the Stanford School of Medicine developed a rapid and highly scalable, deeply targeted sequencing assay for identifying viral fingerprint patterns of SARS-CoV-2 strains isolated from clinical samples. Integral to the success of their game-changing method was the use of the plexWell Library Prep Kits, part of a true multiplexing library prep platform for normalizing next-generation sequencing (NGS) libraries quickly and easily from a large number of samples.

Stanford researchers annotated the signatures of viral mutations associated with specific strains and used these highly conserved viral sequences to identify mutations. To find these highly conserved regions in thousands of samples, the researchers used a novel computational genomics workflow that analyzes short stretches of sequences, known as k-mers, instead of the conventional and time-consuming sequence alignment method.

By analyzing these genetic fingerprints, they were able to identify quasispecies occurring within individual patients and to delineate dominant species and the prevalence of mutation signatures, of which a significant number were relatively unique. By enabling the rapid survey of viral pangenome features such as genome conservation and mutation signatures from thousands of viral samples, the Stanford approach is expected to facilitate molecular contact tracing and comparing viral mutation fingerprints among infected individuals.

plexWell’s kits offer:

  • A true multiplexing library prep platform technology for making normalized next-generation sequencing (NGS) libraries quickly and easily from a large number of samples.
  • Allows multiplexed libraries to be prepared as a single pool after a simple molecular tagging step.
  • Normalizes across a wide range of input DNA or RNA amounts through chemistry.

The plexWell Library Prep Kit’s normalizing library preparation technology allows for the creation of balanced library pools in significantly less time. The simplified 3-hour workflow multiplexes hundreds to thousands of samples for loading in a single sequencing run, resulting in improved overall sequencing performance. This approach consists of an initial reagent-limited tagging step performed on many samples in parallel, coupled with a subsequent pooled library generation step. When these two steps are applied together, they produce approximately equal numbers of library fragments from each of a potentially large collection of samples and allow for a wide repertoire of barcode combinations.

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