TY  - JOUR
AU  - RAMPHAL, UPASANA
AU  - Tshiabuila, Derek
AU  - Ramphal, Yajna
AU  - Giandhari, Jennifer
AU  - van Heerden, Carel
AU  - Baxter, Cheryl
AU  - van Wyk, Stephanie
AU  - Pillay, Sureshnee
AU  - Laguda-Akingba, Oluwakemi
AU  - Wilkinson, Eduan
AU  - Lessells, Richard
AU  - de Oliveira, Tulio
PY  - 2024
DA  - 2024/05/30
TI  - Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant
JO  - OBM Genetics
SP  - 239
VL  - 08
IS  - 02
AB  - During the SARS-CoV-2 pandemic, next-generation sequencing (NGS) technologies like the Ion Torrent S5 and Illumina MiSeq, alongside advanced software, improved genomic surveillance in South Africa. This study analysed anonymized samples from the Eastern Cape using Genome Detective and NextClade, showing Ion Torrent S5 and Illumina MiSeq success rates of 96% and 94%, respectively. The study focused on genomic coverage (above 80%) and mutation detection (below 100), with the Ion Torrent S5 achieving 99% coverage compared to Illumina MiSeq's 80%, likely due to different primers used in amplification. The Ion Torrent S5 was more effective in sequencing varied viral loads, whereas Illumina MiSeq had difficulties with lower loads. Both platforms were adept at identifying clades, successfully differentiating between Beta (
SN  - 2577-5790
UR  - https://doi.org/10.21926/obm.genet.2402239
DO  - 10.21926/obm.genet.2402239
ID  - RAMPHAL2024
ER  -