Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Apr 7:16:1564755.
doi: 10.3389/fmicb.2025.1564755. eCollection 2025.

Viral metagenomics reveals diverse viruses in the fecal samples of children with acute respiratory infection

Pan Xu #  1 , Chunduo Pan #  1 , Minli Yuan  1 , Ying Zhu  1 , Shanjie Wei  1 , Hongyan Lu  1 , Wen Zhang  2
Affiliations

Viral metagenomics reveals diverse viruses in the fecal samples of children with acute respiratory infection

Pan Xu et al. Front Microbiol. .

Abstract

Introduction: Changes in the gut microbiome have been associated with the development of acute respiratory infection (ARI). However, due to methodological limitations, our knowledge of the gut virome in patients with ARIs remains limited.

Methods: In this study, fecal samples from children with ARI were investigated using viral metagenomics.

Results: The fecal virome was analyzed, and several suspected disease-causing viruses were identified. The five viral families with the highest abundance of sequence reads were Podoviridae, Virgaviridae, Siphoviridae, Microviridae, and Myoviridae. Additionally, human adenovirus, human bocavirus, human astrovirus, norovirus, and human rhinovirus were detected. The genome sequences of these viruses were respectively described, and phylogenetic trees were constructed using the gene sequences of the viruses.

Discussion: We characterized the composition of gut virome in children with acute respiratory infections. However, further research is required to elucidate the relationship between acute respiratory infection and gut viruses.

Keywords: acute respiratory infection; children; fecal samples; viral metagenomics; virus evolution.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Taxonomic analysis of fecal virome detected in ARI children on the family level. (A) Heatmap was constructed after transforming read counts per virus family in individual libraries on a log10 scale. Nucleic acid types and virus families are annotated with different colors (see color legend). (B) Bar chart by virus database showing the relative proportion and taxonomy based on viral families.
FIGURE 2
FIGURE 2
The phylogenetic analysis of HAdVs identified in this study. The phylogenetic trees were constructed based on the nearly complete genome of HAdVs that included the reference strains of seven different genotypes. Viruses identified in this study were marked in red font.
FIGURE 3
FIGURE 3
The phylogenetic analysis of HBoVs identified in this study. The phylogenetic trees were constructed based on the nucleotide sequences of NS1 coding region that included the reference strains of three different genotypes. Viruses identified in this study were marked in red font.
FIGURE 4
FIGURE 4
The phylogenetic analysis of HAstVs identified in this study. The phylogenetic trees were constructed based on the nucleotide sequences of ORF2 coding region that included the reference strains of eight different genotypes. Viruses identified in this study were marked in red font.
FIGURE 5
FIGURE 5
The phylogenetic analysis of NoVs identified in this study based on VP1 and RdRp. (A) The phylogenetic trees were constructed based on the nucleotide sequences of VP1 that included the reference strains of seven NoVs genotype. (B) The phylogenetic trees were constructed based on the nucleotide sequences of RdRp that included the reference strains of six NoVs genotype. Viruses identified in this study were marked in red font.
FIGURE 6
FIGURE 6
The phylogenetic analysis of HRV identified in this study. The phylogenetic trees were constructed based on the nucleotide sequences of VP4/VP2 coding region that included the reference strains of three different genotypes. Viruses identified in this study were marked in red font.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Altschul S., Madden T., Schäffer A., Zhang J., Zhang Z., Miller W., et al. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25 3389–3402. 10.1093/nar/25.17.3389 - DOI - PMC - PubMed
    1. Alves J., Teixeira D., Siqueira J., Deus D., Oliveira D., Ferreira J., et al. (2024). Epidemiology and molecular detection of human adenovirus and non-polio enterovirus in fecal samples of children with acute gastroenteritis: A five-year surveillance in northern Brazil. PLoS One 19:e0296568. 10.1371/journal.pone.0296568 - DOI - PMC - PubMed
    1. Antunes K., Fachi J., de Paula R., da Silva E., Pral L., Dos Santos A. Á, et al. (2019). Microbiota-derived acetate protects against respiratory syncytial virus infection through a GPR43-type 1 interferon response. Nat. Commun. 10:3273. 10.1038/s41467-019-11152-6 - DOI - PMC - PubMed
    1. Bender R., Sirota S., Swetschinski A. (2024). Global, regional, and national incidence and mortality burden of non-COVID-19 lower respiratory infections and aetiologies, 1990-2021: A systematic analysis from the Global burden of disease study 2021. Lancet Infect. Dis. 24 974–1002. - PMC - PubMed
    1. Capobianchi M., Giombini E., Rozera G. (2013). Next-generation sequencing technology in clinical virology. Clin. Microbiol. Infect. 19 15–22. 10.1111/1469-0691.12056 - DOI - PubMed

LinkOut - more resources