{"doi":"10.1371/journal.pone.0283219","title":"Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing","abstract":"The global pandemic caused by SARS-CoV-2 has increased the demand for scalable sequencing and diagnostic methods, especially for genomic surveillance. Although next-generation sequencing has enabled large-scale genomic surveillance, the ability to sequence SARS-CoV-2 in some settings has been limited by the cost of sequencing kits and the time-consuming preparations of sequencing libraries. We compared the sequencing outcomes, cost and turn-around times obtained using the standard Illumina DNA Prep kit protocol to three modified protocols with fewer clean-up steps and different reagent volumes (full volume, half volume, one-tenth volume). We processed a single run of 47 samples under each protocol and compared the yield and mean sequence coverage. The sequencing success rate and quality for the four different reactions were as follows: the full reaction was 98.2%, the one-tenth reaction was 98.0%, the full rapid reaction was 97.5% and the half-reaction, was 97.1%. As a result, uniformity of sequence quality indicated that libraries were not affected by the change in protocol. The cost of sequencing was reduced approximately seven-fold and the time taken to prepare the library was reduced from 6.5 hours to 3 hours. The sequencing results obtained using the miniaturised volumes showed comparability to the results obtained using full volumes as described by the manufacturer. The adaptation of the protocol represents a lower-cost, streamlined approach for SARS-CoV-2 sequencing, which can be used to produce genomic data quickly and more affordably, especially in resource-constrained settings.","journal":"PLoS ONE","year":2023,"id":359309,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":10,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9479,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":287019,"name":"James Emmanuel San","orcid":null,"position":1,"is_corresponding":false},{"id":621554,"name":"Derek Tshiabuila","orcid":"0000-0001-5221-2126","position":2,"is_corresponding":false},{"id":838674,"name":"Yeshnee Naidoo","orcid":"0000-0002-9040-963X","position":3,"is_corresponding":false},{"id":839035,"name":"Yusasha Pillay","orcid":"0009-0008-6442-7296","position":4,"is_corresponding":false},{"id":840499,"name":"Akhil Maharaj","orcid":null,"position":5,"is_corresponding":false},{"id":838658,"name":"Ugochukwu J. Anyaneji","orcid":"0000-0002-3445-2633","position":6,"is_corresponding":false},{"id":282133,"name":"Eduan Wilkinson","orcid":"0000-0002-2503-9441","position":7,"is_corresponding":false},{"id":282134,"name":"Houriiyah Tegally","orcid":"0000-0002-7102-8540","position":8,"is_corresponding":false},{"id":69666,"name":"Richard Lessells","orcid":"0000-0003-0926-710X","position":9,"is_corresponding":false},{"id":536857,"name":"Cheryl Baxter","orcid":"0000-0002-6033-7655","position":10,"is_corresponding":false},{"id":279259,"name":"Túlio de Oliveira","orcid":"0000-0002-3027-5254","position":11,"is_corresponding":false},{"id":282131,"name":"Jennifer Giandhari","orcid":"0000-0002-2944-4583","position":12,"is_corresponding":false},{"id":282132,"name":"Sureshnee Pillay","orcid":"0000-0001-9288-7996","position":0,"is_corresponding":true}],"reference_count":24,"raw_metadata":null,"created_at":"2026-07-19T01:13:52.889556Z","pmid":"37099540","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}