SUB-GENOMIC RNA EXPRESSION IN SARS-COV-2 OMICRON INFECTIONS IN SRI LANKA

Abstract

Intro: Sri Lanka detected the first infection due to BA.1 back in November 2021, which was quickly replaced by BA.2 by end of January. With detection of BA.5.2 in late June 2022, the number of symptomatic cases has increased without a similar increase in mortality rates as seen with BA.1 and BA.2. Therefore, we compared sgRNA expression of each protein between the omicron sub-lineages to determine any differences that could be contributing to viral virulence. Methods: Nasopharyngeal samples of 925 patients with SARS-CoV-2 infection sequenced at our laboratory between November 2021 to August 2022 were included in the analysis. Samples were sequenced using the Midnight protocol on Oxford Nanopore MinION. The resulting data was analyzed and assigned to lineages using wf-artic pipeline. Fastq data were re-analyzed by periscope (https://github.com/sheffield-bioinformatics-core/periscope) in order to identify sub-genomic RNA reads. Means of sgRNA counts normalized to per 1000 genomic RNA reads were compared for each ORF using an unpaired Wilcoxon test adjusting p-values with the Holm method. Findings: Out of 724 Omicron datasets that passed the quality control, 162 were BA.1, 482 were BA.2, and 80 were BA.5 sub-lineages. BA.2 viruses appear to have significantly higher sgRNA in the spike, envelope, and membrane protein while, BA.5 viruses have significantly high levels of sgRNA in their ORF3a, ORF7a, ORF8, and ORF10 proteins. Interestingly, sgRNA expression of nucleocapsid protein is significantly lower in BA.5 compared to BA.1 and BA.2. Conclusion: Our results suggest that significantly low sgRNA expression in spike, envelope, membrane, ORF6, and nucleocapsid proteins of BA.5 could have been a fitness disadvantage while higher sgRNA levels in ORF7a, ORF8, and ORF10 could have enhanced immunomodulation and immune evasion of BA.5 compared to the other two Omicron sub-lineages in Sri Lanka.