Genomic Epidemiology of SARS-CoV-2 variants in unvaccinated children found to be similar to that of adults with COVID-19 vaccinations

Key Points

• The central aim is to investigate the phylogenetic diversity of SARS-CoV-2 variants in relation to children's age and vaccination status.
• Analyzed 569 SARS-CoV-2 genome sequences across Pakistan from May 2021 to October 2022.
• Collected metadata including age, sex, and vaccination status from GISAID.
• Conducted phylogenetic analyses using the Augur pipeline and visualized data with Auspice.
• Assessed viral load from Ct values of PCR diagnostic assays for 143 pediatric samples.
• Delta variant was predominant at 45.2% in 2021, while Omicron was at 45.9% in 2022.
• 71% of sequences were from individuals under 18 years; only 29.3% of those were vaccinated.
• No significant difference was found in variant distribution between vaccinated and unvaccinated individuals (p=0.75).
• Omicron variants were linked to higher viral loads (p<0.001).