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Background <p>Human bocavirus (HBoV) is frequently detected in pediatric respiratory infections, yet its molecular epidemiology and genomic diversity remain incompletely characterized in many regions. We investigated HBoV circulation among hospitalized children with pneumonia in Suzhou, China, from 2022 to 2025 and assessed VP1/VP2 variation for potential physicochemical and functional impacts.</p> Methods <p>Oropharyngeal swabs were collected from hospitalized pediatric pneumonia cases and screened for HBoV using multiplex real-time PCR. HBoV-positive samples with Ct &lt; 30 were subjected to amplicon-based whole-genome sequencing using a 17-primer-pair scheme covering &gt; 98% of the genome, followed by assembly and comparative genomic analysis. Genotyping was performed by maximum-likelihood phylogenetic inference based on VP1/VP2 sequences. Deduplicated VP1/VP2 amino acid sequences were analyzed for hydrophobicity (ProtScale, Kyte–Doolittle, window = 9) and predicted functional impact (PROVEAN, cutoff − 2.5).</p> Results <p>Among 1,372 specimens, 83 were HBoV-positive (6.05%), with increased detection in autumn (September–November). Co-detection of other respiratory pathogens occurred in 59/83 (71.08%) samples. The most frequently co-detected pathogens were human rhinovirus (27/83, 32.53%), Haemophilus influenzae (13/83, 15.66%), respiratory syncytial virus (13/83, 15.66%), and Streptococcus pneumoniae (13/83, 15.66%). We obtained 45 complete HBoV genomes (6 in 2022, 5 in 2023, 15 in 2024, and 19 in 2025). VP1/VP2 phylogenetic analysis classified all strains as HBoV-1 and further into subclades Ⅰa (<i>n</i> = 6) and Ⅰb (<i>n</i> = 39), with Ⅰb predominating. Nucleotide substitutions and amino acid changes were mainly concentrated in the VP1/VP2 region. Hydrophobicity profiles of VP1/VP2 were largely conserved relative to reference strains, with only local shifts adjacent to substitution sites. PROVEAN predicted major substitutions (e.g., R17K, A149T, T590S) as neutral.</p> Conclusions <p>HBoV was detected in 6.05% of hospitalized children with pneumonia in Suzhou during 2022–2025, with frequent co-detections. Genomic surveillance based on 45 complete genomes indicates the predominance of HBoV-1 subclade Ⅰb, and VP1/VP2 variation was mainly capsid-region–enriched but exhibited overall stable hydrophobicity patterns and largely neutral predicted functional impacts. These findings provide a genomic baseline for continued molecular surveillance in the region.</p>

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Molecular epidemiology and whole-genome characterization of human bocavirus in hospitalized children with pneumonia in Suzhou, China, 2022–2025

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  • 发表日期：

    2026年4月4日

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  • Xuan Yuan,
  • Yayun Tan,
  • Zhihui Xu,
  • Xuerong Ya,
  • Zefeng Dong,
  • Qiang Shen

摘要

Background

Human bocavirus (HBoV) is frequently detected in pediatric respiratory infections, yet its molecular epidemiology and genomic diversity remain incompletely characterized in many regions. We investigated HBoV circulation among hospitalized children with pneumonia in Suzhou, China, from 2022 to 2025 and assessed VP1/VP2 variation for potential physicochemical and functional impacts.

Methods

Oropharyngeal swabs were collected from hospitalized pediatric pneumonia cases and screened for HBoV using multiplex real-time PCR. HBoV-positive samples with Ct < 30 were subjected to amplicon-based whole-genome sequencing using a 17-primer-pair scheme covering > 98% of the genome, followed by assembly and comparative genomic analysis. Genotyping was performed by maximum-likelihood phylogenetic inference based on VP1/VP2 sequences. Deduplicated VP1/VP2 amino acid sequences were analyzed for hydrophobicity (ProtScale, Kyte–Doolittle, window = 9) and predicted functional impact (PROVEAN, cutoff − 2.5).

Results

Among 1,372 specimens, 83 were HBoV-positive (6.05%), with increased detection in autumn (September–November). Co-detection of other respiratory pathogens occurred in 59/83 (71.08%) samples. The most frequently co-detected pathogens were human rhinovirus (27/83, 32.53%), Haemophilus influenzae (13/83, 15.66%), respiratory syncytial virus (13/83, 15.66%), and Streptococcus pneumoniae (13/83, 15.66%). We obtained 45 complete HBoV genomes (6 in 2022, 5 in 2023, 15 in 2024, and 19 in 2025). VP1/VP2 phylogenetic analysis classified all strains as HBoV-1 and further into subclades Ⅰa (n = 6) and Ⅰb (n = 39), with Ⅰb predominating. Nucleotide substitutions and amino acid changes were mainly concentrated in the VP1/VP2 region. Hydrophobicity profiles of VP1/VP2 were largely conserved relative to reference strains, with only local shifts adjacent to substitution sites. PROVEAN predicted major substitutions (e.g., R17K, A149T, T590S) as neutral.

Conclusions

HBoV was detected in 6.05% of hospitalized children with pneumonia in Suzhou during 2022–2025, with frequent co-detections. Genomic surveillance based on 45 complete genomes indicates the predominance of HBoV-1 subclade Ⅰb, and VP1/VP2 variation was mainly capsid-region–enriched but exhibited overall stable hydrophobicity patterns and largely neutral predicted functional impacts. These findings provide a genomic baseline for continued molecular surveillance in the region.