Automated Library Construction and Analysis for High-throughput Nanopore Sequencing of SARS-CoV-2

J Appl Lab Med. 2022 Jun 20;jfac054. doi: 10.1093/jalm/jfac054. Online ahead of print.

Abstract

Background: To support the implementation of high-throughput pipelines suitable for SARS-CoV-2 sequencing and analysis in a clinical laboratory, we developed an automated sample preparation and analysis workflow.

Methods: We used the established ARTIC protocol with ∼400 bp amplicons sequenced on Oxford Nanopore's MinION. Sequences were analyzed using Nextclade, assigning both a clade and quality score to each sample.

Results: 2,179 samples on twenty-five 96-well plates were sequenced. Plates of purified RNA were processed within 12 hours, sequencing required up to 24 hours and analysis of each pooled plate required one hour. The use of samples with known Ct values enabled normalization, acted as a QC check, and revealed a strong correlation between sample Ct values and successful analysis, with 85% of samples with Ct < 30 achieving a "Good" Nexclade score. Less abundant samples responded to enrichment with the fraction of Ct > 30 samples achieving a "Good" classification rising by 60% after addition of a post-ARTIC PCR normalization. Serial dilutions of three variant of concern samples, diluted from Ct∼16 to Ct∼50, demonstrated successful sequencing to Ct 37. The sample set contained a median of 24 mutations per sample and a total of 1,281 unique mutations with reduced sequence read coverage noted in some regions of some samples. A total of ten separate strains were observed in the sample set, including three variants of concern prevalent in British Columbia in the spring of 2021.

Conclusions: We demonstrated a robust automated sequencing pipeline that takes advantage of input Ct values to improve reliability.