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bioRxiv · 10.1101/2022.11.07.515545

Optimization of the Illumina COVIDSeq™ protocol for decentralized, cost-effective genomic surveillance

Carpenter, R. E.·Tamrakar, V. K.·Almas, S.·Rowan, C.·Sharma, R.
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Abstract

A decentralized surveillance system to identify local outbreaks and monitor SARS-CoV-2 Variants of Concern is one of the primary strategies for the pandemics containment. Although next-generation sequencing (NGS) is a gold standard for genomic surveillance and variant discovery, the technology is still cost-prohibitive for decentralized sequencing, particularly in small independent labs with limited resources. We have optimized the Illumina COVID-seq protocol to reduce cost without compromising accuracy. 90% of genomic coverage was achieved for 142/153 samples analyzed in this study. The lineage was correctly assigned to all samples (152/153) except for one. This modified protocol can help laboratories with constrained resources contribute to decentralized SARS-CoV-2 surveillance in the post-vaccination era.

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Carpenter, R. E., Tamrakar, V. K., Almas, S., Rowan, C., Sharma, R.. 2022-11-08. Optimization of the Illumina COVIDSeq™ protocol for decentralized, cost-effective genomic surveillance. https://doi.org/10.1101/2022.11.07.515545

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