| Summary: | Human <i>Anelloviridae</i> is a highly prevalent viral family, including three main genera—<i>Alphatorquevirus</i> (Torque teno virus, TTV), <i>Betatorquevirus</i> (Torque teno mini virus, TTMV), and <i>Gammatorquevirus</i> (Torque teno midi virus, TTMDV). To date, the characterization of <i>Anelloviridae</i> in the respiratory tract of children with acute respiratory infection (ARI) has been poorly reported and mainly focused on TTV. We performed a metagenomic analysis of eight respiratory samples collected from children with an ARI of unknown etiology (eight samples tested negative with a multiplex PCR assay, out of the 39 samples initially selected based on negative routine diagnostic testing). A total of 19 pediatric respiratory samples that tested positive for respiratory syncytial virus (RSV, <i>n</i> = 13) or influenza virus (<i>n</i> = 6) were also sequenced. <i>Anelloviridae</i> reads were detected in 16/27 samples, including 6/8 negative samples, 7/13 RSV samples and 3/6 influenza samples. For samples with a detection of at least one <i>Anelloviridae</i> genus, TTMV represented 87.1 (66.1–99.2)% of <i>Anelloviridae</i> reads, while TTV and TTMDV represented 0.8 (0.0–9.6)% and 0.7 (0.0–7.1)%, respectively (<i>p</i> < 0.001). Our findings highlight a high prevalence of TTMV in respiratory samples of children with an ARI of unknown etiology, as well as in samples with an RSV or influenza infection. Larger studies are needed to explore the role of TTMV in childhood respiratory diseases.
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