In vitro fitness of SARS-CoV-2 variants as assessed by competition experiments followed by ddRT-PCR and whole genome sequencing

Objective: To develop a new method for reliable and rapid determination of the fitness of SARS-CoV-2 variants of concern. Methods: Competition experiments between two SARS-CoV-2 variants were performed in cells of the upper (nasal human airway epithelium) and lower (Calu-3 cells) respiratory tracts followed by quantification of variant ratios by droplet digital reverse transcription (ddRT)-PCR.Results: In competition experiments, the delta variant outcompeted the alpha variant in both cells of the upper and lower respiratory tracts. A 50/50% mixture of delta and omicron variants indicated a predominance of omicron in the upper respiratory tract whereas delta predominated in the lower respiratory tract. There was no evidence of recombination events between variants in competition as assessed by whole gene sequencing.Conclusion: Differential replication kinetics were shown between variants of concern which may explain, at least partly, the emergence and disease severity associated with new SARS-CoV-2 variants.

Automated summary

Objective: A new method for determining the fitness of SARS-CoV-2 variants of concern was developed. Methods: Competition experiments between two variants were conducted in cells of the upper and lower respiratory tracts, followed by quantification of variant ratios using ddRT-PCR. Results: The delta variant outcompeted the alpha variant in both upper and lower respiratory tract cells. A 50/50% mixture of delta and omicron variants indicated a predominance of omicron in the upper respiratory tract and delta in the lower respiratory tract. No evidence of recombination events between variants was found through whole gene sequencing analysis. Conclusion: Variants of concern showed differential replication kinetics, which may partially explain the emergence and disease severity associated with new SARS-CoV-2 variants.