Comparative Analysis of Subgenomic RNA Profiles across SARS-CoV-2 lineages in Hong Kong - Part 1

This dataset comprises raw sequencing data from a large-scale genomic study of SARS-CoV-2 clinical samples collected in Hong Kong between 2020 and 2022. The study aimed to characterise lineage-specific expression profiles of subgenomic RNAs (sgRNAs), which are critical for viral replication and pathogenesis. Data cover major pandemic lineages, including 20A, 20B, Alpha, Delta, and Omicron subvariants (BA.1, BA.2, BA.4, BA.5, XBB).Samples were processed at a WHO reference laboratory at the University of Hong Kong. RNA was reverse-transcribed and amplified using ARTIC V4.1 primers and a set of in-house gene-specific primers. Libraries were sequenced on Novaseq or iSeq100 platforms. This dataset provides a fundamental resource for investigating the transcriptional dynamics of SARS-CoV-2 across variants, with particular relevance to sgRNA function, viral evolution, and comparative lineage studies.