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. 2023 Apr 19;20(1):74.
doi: 10.1186/s12985-023-02019-w.

Molecular characterization of coxsackievirus B5 from the sputum of pneumonia children patients of Kunming, Southwest China

Miao Tan #  1   2 , Jiale Suo #  3   2 , Zhilei Zhang #  4   5 , Wenji He  4 , Li Tan  4 , Haiyan Jiang  4   5 , Ming Li  4 , Juan He  4 , Yue Pan  3   6 , Bin Xu  4 , Lingmei Yan  3   6 , Songtao Bin  4 , Zhengyan Gan  4 , Yuxing Sun  4 , Hongchao Jiang  7   8 , Qiangming Sun  9   10 , Zhen Zhang  11
Affiliations

Molecular characterization of coxsackievirus B5 from the sputum of pneumonia children patients of Kunming, Southwest China

Miao Tan et al. Virol J. .

Abstract

Background: CVB5 can cause respiratory infections. However, the molecular epidemiological information about CVB5 in respiratory tract samples is still limited. Here, we report five cases in which CVB5 was detected in sputum sample of pneumonia children patients from Kunming, Southwest China.

Methods: CVB5 isolates were obtained from sputum samples of patients with pneumonia. Whole-genome sequencing of CVB5 isolates was performed using segmented PCR, and phylogenetic, mutation and recombination analysis. The effect of mutations in the VP1 protein on hydration were analyzed by Protscale. The tertiary models of VP1 proteins were established by Colabfold, and the effect of mutations in VP1 protein on volume modifications and binding affinity were analyzed by Pymol software and PROVEAN.

Results: A total of five CVB5 complete genome sequences were obtained. No obvious homologous recombination signals comparing with other coxsackie B viruses were observed in the five isolates. Phylogenetic analysis showed that the five CVB5 sputum isolates were from an independent branch in genogroup E. Due to the mutation, the structure and spatial of the VP1 protein N-terminus have changed significantly. Comparing to the Faulkner (CVB5 prototype strain), PROVEAN revealed three deleterious substitutions: Y75F, N166T (KM35), T140I (KM41). The last two of the three deleterious substitutions significantly increased the hydrophobicity of the residues.

Conclusions: We unexpectedly found five cases of CVB5 infection instead of rhinoviruses infection during our routine surveillance of rhinoviruses in respiratory tract samples. All five patients were hospitalized with pneumonia symptoms and were not tested for enterovirus during their hospitalization. This report suggests that enterovirus surveillance in patients with respiratory symptoms should be strengthened.

Keywords: Analysis; CVB5; Epidemiology; Pneumonia.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Phylogeny of CVB5 isolates based on the VP1 generated by the N-J method implemented in MEGA 5.0. The three isolates in red were highly similar to five sputum isolates and nine fecal isolates. The black circles indicate CVB5 isolates from fecal samples. The black triangles indicate CVB5 isolates from the sputum samples
Fig. 2
Fig. 2
Similarity plot of the VP1 sequences of KM34, KM35, KM40, KM41 and KM48 compared to the Faulkner, and 2018 fecal isolates
Fig. 3
Fig. 3
Similarity plot of the complete genome sequences of KM34, KM35, KM40, KM41 and KM48 comparing to other CVBs strains. Each point represents the similarity between the query sequence, with a 200-nt window moving in 20-nt steps. Positions containing gaps were excluded from the analysis
Fig. 4
Fig. 4
Amino acid mutations of the KM34, KM35, KM40, KM41, and KM48 isolates compared with the Faulkner (a) and 2018 fecal isolates (b)
Fig. 5
Fig. 5
Aligned Faulkner, KM35 and KM41 with Pymol. Alignment diagram of Faulkner (green) and KM35 (blue). a Alignment diagram of Faulkner (green) and KM41 (red) (b)
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