A decentralized surveillance system to identify local outbreaks and monitor SARS-CoV-2 Variants of Concern is one of the primary strategies for the pandemic’s containment. Although nextgeneration 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 COVIDSeq™ protocol for the Illumina MiniSeq instrument to reduce cost without compromising accuracy. We slashed the library preparation cost by half by using 50% of recommended reagents at each step and normalizing the libraries before pooling to achieve uniform coverage. Reagent-only cost (~ $43.27/sample) for SARS-CoV-2 variant analysis with this normalized input protocol on MiniSeq instruments is comparable to what is achieved on high throughput instruments such as NextSeq and NovaSeq. Using this modified protocol, we tested 153 clinical samples, and 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 to contribute in decentralized COVID-19 surveillance in the postvaccination era.


© 2023 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).



Date of publication

Spring 2-1-2023



Persistent identifier


Document Type


Publisher Citation

Rob E. Carpenter, Vaibhav K. Tamrakar, Sadia Almas, Aditya Sharma, Chase Rowan, Rahul Sharma, Optimization of the Illumina COVIDSeq™ protocol for decentralized, cost-effective genomic surveillance.Practical Laboratory Medicine, 2023,Volume 34:e00311. ISSN 2352-5517. https://doi.org/10.1016/j.plabm.2023.e00311.