Genetic diversity of Microviridae phages in the human respiratory tract

Recent studies have revealed that Microviridae, a family of ssDNA viruses, are widely distributed in natural environments and play significant roles in various ecosystems. While Microviridae members dominate the human gut microbiome, their genetic diversity in the human respiratory ecosystem remains unclear. The distribution, genetic characteristics, and ecological roles of Microviridae are still poorly understood. This study identified 327 Microviridae-associated contigs from nasopharyngeal swab samples of healthy individuals through metagenomic sequencing and comparative genomics analysis, including 15 near-complete Microviridae-related genomes. These genomes exhibited high sequence divergence from each other, revealing their high genetic diversity. Phylogenetic analysis based on VP1 (major capsid protein; F protein) demonstrated that the 15 genomes could be classified into seven distinct Microviridae groups. CRISPR spacer matching predicted the host of the 15 genomes. The total read counts of Microviridae across all 12 libraries were quantified and compared using the Kruskal-Wallis test. This work significantly expands the understanding of the diversity, genomic architecture, and evolutionary dynamics of Microviridae within the human respiratory tract.