Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases

Antonio Lentini¹, Antonio Pereira², Ola Winqvist², Björn Reinius¹

¹ Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

² ABC Labs, Biomedicum, Stockholm, Sweden.

Abstract

Throughout the SARS-CoV-2 pandemic, multiple waves of variants of concern have swept across populations, leading to a chain of new and yet more contagious lineages dominating COVID-19 cases. Here, we tracked the remarkably rapid shift from Omicron BA.1 to BA.2 sub-variant dominance in the Swedish population during January–March 2022. By analysis of 174,933 clinical nasopharyngeal swab samples using a custom variant-typing RT-PCR assay, we uncover nearly two-fold higher levels of viral RNA in cases with Omicron BA.2. Importantly, increased viral load in the upper pharynx upon BA.2 infection may provide part of the explanation why Omicron BA.2 is more transmissible and currently outcompetes the BA.1 variant across populations.

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This repository contains code to reproduce findings in our [PRE-PRINT](https://doi.org/10.1101/2022.03.26.22272984; Pending publication in Med https://www.cell.com/med/), raw sequencing data is available in E-MTAB-11650 and assembled genomes are available under accessions EPI_ISL_11414777 - 11415389 and EPI_ISL_11450500 - 11450677) at GISAID