Fitness of SARS-CoV-2 Omicron Subvariants in Respiratory and Gastrointestinal Cell Lines as Determined by Reverse-Transcription Droplet Digital PCR and Whole-Genome Sequencing.

Abstract

The fitness of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants was determined in human epithelial and continuous cells of the respiratory and gastrointestinal tracts. Competition experiments over 4 days were performed followed by quantification of variant ratios by reverse transcription-droplet digital PCR. These quantitative data were correlated with whole-genome sequencing. In competition experiments of 2 subvariants, the more recent XBB.1 subvariant outcompeted the BA.1.15 subvariant at early time points in the upper respiratory tract epithelium. No difference in replication was observed between the 2 subvariants in the lower respiratory tract. Furthermore, XBB.1 predominated over BA.1.15 and JN.1.1 subvariants in the gastrointestinal tract.