Fig. 3. Detailed profile of microbial diversity.

A Alpha-diversity (richness) among the Covid-19 cases and healthy controls (HC) were estimated through Shannon diversity index (SDI). The SDI among the cases and HC were depicted through violin plots. B Violin plots of SDI between cases and HC at different time points, such as Day 1, Day 15, and Day 30. The cases of Day 30 were divided into two distinct sub-groups: Group A, RT-PCR positive, and Group B, RT-PCR negative. C The principal components (PC1 vs PC2) plot is based on the Jaccard diversity index and demonstrates microbial clustering among groups (Aand B) across different time points (Day 1, Day 15 and Day 30) as well as HC. D Heat map showing the intra-individual beta diversity of the human oropharyngeal microbiome among groups estimated through Bray-Curtis Diversity Index.