The fitness of 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 two 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 two subvariants in the lower respiratory tract. Furthermore, XBB.1 predominated over BA.1.15 and JN.1.1 subvariants in the gastrointestinal tract.
Keywords: Omicron subvariant; RT-ddPCR; SARS-CoV-2; competition; fitness.
Published by Oxford University Press on behalf of Infectious Diseases Society of America 2024.