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

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.

Molecular Characterization of the Viral Structural Genes of Human Rhinovirus A11 from Children Hospitalized with Lower Respiratory Tract Infection in Kunming.

BACKGROUND: The human rhinovirus (HRV) is a picornavirus that can cause a variety of respiratory diseases, including the aggravation of chronic respiratory diseases, such as bronchitis, pneumonia, and asthma. Although an increasing number of lower respiratory tract infection cases have been reported with HRV infection in Europe, few such cases have been reported in China. METHODS: The complete genomic sequences of the HRV-A11 epidemic strains were amplified and obtained by segmented polymerase chain reaction (PCR) and sequence, and then the phylogenetic, nucleotide mutation, recombinant, and comparative analyses of amino acid mutations were performed. RESULTS: Phylogenetic analyses showed that the epidemic strains from 3 rare cases of pneumonia belong to the HRV-A11 subgenotypes. All strains were highly similar to strains from the United States. No obvious homologous recombination signals were observed in the epidemic strains. There were 498 nucleotide and 47 amino acid mutations compared with the HRV-A11 prototype strain. Amino acid mutations were observed at the capsid protein region, P1a, RVA2147-2155, and RVA97-114 epitopes of these clinical strains. CONCLUSIONS: We reported the first case of HRV-A11-associated lower respiratory tract infection in China. These mutations in the P1a, HRV A-specific CD8, and CD4 T-cell epitopes might provide a reference for virological surveillance and vaccine development.