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Objective To predict and analyze the physicochemical properties, structural characteristics, and antigenic epitopes of viral protein (VP) VP1 of Coxsackievirus A10 (CV-A10) by bioinformatics methods. Methods The physicochemical properties and structural characteristics of CV-A10 VP1 were predicted by ProtParam, SOPMA, SWISS-MODEL, PDBsum, and ProSA-web. The antigenic epitopes of CV-A10 VP1 were predicted and analyzed by DNAstar, ABCpred, Bepipred 2.0, ElliPro, DiscoTope-2.0, NetMHCpan-4.1, NetMHCIIpan-4.0, Consurf, VaxiJen v.2.0, AllerTOP v.2.0, ToxinPred2, and IEDB immunogenicity. Results Bioinformatics analysis showed that CV-A10 VP1 was a basic, unstable, and hydrophilic protein, of which the secondary structure mainly consisted of random coil. The analysis revealed that CV-A10 VP1 had multiple potential B and T cell antigenic epitopes as well as a dominant antigenic epitope based on the potential epitope. Conclusion CV-A10 VP1 has multiple potential sites that induce specific humoral and cellular immunity, providing important support for its experimental identification, molecular epidemiological studies, and vaccine development.
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Objective@#To investigate the etiology spectrum of hand foot and mouth disease (HFMD) and to analyze the molecular characteristics of Coxsackievirus A10 and A6 in Qingdao in 2014.@*Methods@#Throat swabs of HFMD cases were tested for total enteroviruses (EVs), EV-A71, CV-A16, CV-A10 and CV-A6 by multiplex real time RT-PCR. Other EV serotypes were identified through the sequences of partial VP1 gene. The full-length of VP1 gene of CV-A10 and CV-A6 were amplified and sequenced. The sequences were phylogenetically analyzed using MEGA 5.0 software package.@*Results@#A total of 1727 HFMD patients were detected in 2014 and 11serotypes of enteroviruses were identified. EV-A71(38.0%, 410/1078), CV-A16(28.8%, 311/1078), CV-A10(14.1%, 152/1078)and CV-A6(3.2%, 34/1078)were the most dominant pathogen in 2014 in Qingdao. Proportions of CV-A10 in enterovirus infected children varied dramatically in different ages(χ2=15.19, P=0.001), showing a downtrend with age. Proportion of CV-A10 in inpatients was much higher than that in outpatients(χ2=49.1, P <0.001), while 60% of those inpatients showed nervous system damage symptoms, with pathological reflex or disappearance of physiological reflex. Phylogenetic analysis of complete VP1 sequences showed that all CV-A10 strains identied in this study belonged to genotype C, 71.7% of which located in branch C5; all CV-A6 strains belonged to genotype D while 83.3% of which located in branch D5.@*Conclusions@#EV-A71, CV-A16, CV-A10 and CV-A6 were the prevalent pathogens of HFMD in Qingdao in 2014. CV-A10 was more frequently detected in lower age group with HFMD, which can cause damage to nervous system. Strains of branch C5 in genotype C were the dominant strains of CV-A10 circulated in Qingdao in 2014 while strains of branch D5 in genotype D were the major strains of CV-A6.
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Objective To detect and analyze enteroviruses causing suspected aseptic meningitis in a kindergarten in Jinhua City, Zhejiang Province. Methods Viral RNA was extracted from samples and cDNA was prepared by reverse transcription. PCR was performed to amplify the partial sequences of the 5′-untranslated region ( UTR) and VP1 gene of enteroviruses. Serotypes of the viruses were determined by com-paring the homology between the partial sequences of VP1 gene. Phylogenetic tree of the partial VP1 se-quences was constructed using MEGA6. Results This study included seven patients and twenty-six asymp-tomatic students. Coxsakievirus A10 (CV-A10) was detected in 48. 5％ of the students and echovirus 6 (Echo 6) in 21. 2％. Besides, 12. 1％ of the students might be co-infected by the two viruses. Among the seven patients, six were infected by CV-A10 and the other one might have co-infection. According to the phylogenetic analysis, CV-A10 strains detected in this study were closely related to those isolated in China in recent years, including the strains isolated in Xiamen in 2015 and Yunnan in 2017, while the Echo 6 strains were phylogenetically related to those isolated in Yunnan, Guangzhou and Shandong in 2014. Conclusions CV-A10 and Echo 6 were detected in the cases with suspected aseptic meningitis and had close phylogenetic relationships to the strains appeared in China in recent years.
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Objective To study the genetic characteristics of VP1 region of coxsackievirus A10(Cox A10) strains isolated from hand foot and mouth disease (HFMD) cases in Ningxia Hui Autonomous Region(Ningxia)in 2013. Methods A total of 280 specimens,which were identified as non-enterovirus 71 and non-Cox A16 by real-time PCR,were collected and cultured by using RD cell,and the VP1 genes of isolated strains were amplified by using reverse transcriptase PCR (RT-PCR) with degenerated primers and sequenced. The sequencing results were aligned with the sequences in GenBank with BLAST algorithm to identify the virus genotypes. Homologous comparison and phylogenetic analysis were conducted for all the Cox A10 strains identified. Results Among 36 virus strains isolated from 280 clinical specimens,6 were identified as Cox A10. The homologies of nucleotide and amino acid of the Cox A10 strains isolated in Ningxia were 97.0%-99.8% and 99.0%-99.7% respectively,and the Cox A10 strains isolated in Ningxia shared 76.3%-77.2%,81.6%-83.1%,94.4%-98.9% and 80.0%- 82.3% nucleotide homologies respectively and shared 92.3%-93.0%,94.0%-95.3%,98.0%-99.7% and 90.6%-94.0% amino acid homologies respectively with the representative strains of A,B,C and D genotypes. Phylogenetic tree analysis revealed that Cox A10 strains isolated in Ningxia belonged to genotype C. Conclusion Cox A10 is one of the most common pathogen causing HFMD in Ningxia in 2013. All the Cox A10 stains isolated from HFMD patients in Ningxia belonged to genotype C.
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Objective To study the genetic characteristics of VP1 region of coxsackievirus A10(Cox A10) strains isolated from hand foot and mouth disease (HFMD) cases in Ningxia Hui Autonomous Region(Ningxia)in 2013. Methods A total of 280 specimens,which were identified as non-enterovirus 71 and non-Cox A16 by real-time PCR,were collected and cultured by using RD cell,and the VP1 genes of isolated strains were amplified by using reverse transcriptase PCR (RT-PCR) with degenerated primers and sequenced. The sequencing results were aligned with the sequences in GenBank with BLAST algorithm to identify the virus genotypes. Homologous comparison and phylogenetic analysis were conducted for all the Cox A10 strains identified. Results Among 36 virus strains isolated from 280 clinical specimens,6 were identified as Cox A10. The homologies of nucleotide and amino acid of the Cox A10 strains isolated in Ningxia were 97.0%-99.8% and 99.0%-99.7% respectively,and the Cox A10 strains isolated in Ningxia shared 76.3%-77.2%,81.6%-83.1%,94.4%-98.9% and 80.0%- 82.3% nucleotide homologies respectively and shared 92.3%-93.0%,94.0%-95.3%,98.0%-99.7% and 90.6%-94.0% amino acid homologies respectively with the representative strains of A,B,C and D genotypes. Phylogenetic tree analysis revealed that Cox A10 strains isolated in Ningxia belonged to genotype C. Conclusion Cox A10 is one of the most common pathogen causing HFMD in Ningxia in 2013. All the Cox A10 stains isolated from HFMD patients in Ningxia belonged to genotype C.
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Objective To analyze the etiologic spectrum of hand, foot and mouth disease (HFMD) and the molecular characteristics of coxsackievirus A10 (CVA10) strains isolated in Qingdao from year 2010 to 2012.Methods Throat swab specimens were collected from patients with HFMD to detect to-tal enteroviruses ( EVs) , EV71 and CVA16 strains by multiplex real time RT-PCR.The EV-positive speci-mens were further detected by a semi-nested RT-PCR to amplify the sequence of viral genes encoding VP1. The serotypes of EVs were identified based on the sequences of genes encoding VP1.The full-length gene se-quences encoding VP1 of CVA10 isolates were amplified and sequenced. The phylogenetic analysis was con-ducted by using MEGA5.0 software package.Results A total of 1919 outpatients with mild HFMD and 1336inpatients with serious HFMD were recruited in this study .CVA16 strains were the predominant patho-gen for outpatients in year 2010 ( prevalence rate of 53%) and 2012 ( prevalence rate of 73%) .EV71 strains were the predominant pathogen for outpatients in year 2011 ( prevalence rate of 78%) and inpatients in year 2010 ( prevalence rate of 70%) and 2011 ( prevalence rate of 86%) . Some serotypes other than CVA16 or EV71 were the predominant pathogens for inpatients in year 2012 ( prevalence rate 44%) . CVA10 strains were identified in 12 patients with HFMD in year 2010and 17 patients with HFMD in 2012. The full-length gene sequences encoding VP1 of 23 CVA10 isolates were successfully amplified and se-quenced.The phylogenetic analysis showed that the 23 CVA10 isolates all belonged to genotype C and could be further divided into six clades.The genes encoding VP1 of the 23 CVA10 strains shared 97.3% to 1000.%homologies in amino acid sequences.The CVA10 isolates were also similar to their counterparts isolated from other regions during the same period.Conclusion CVA16 and EV71 strains were the preva-lent pathogens of HFMD in Qingdao from year 2010 to 2012, co-circulated with some other serotypes of EVs, especially CVA10 strains.The CVA10 strains belonged to genotype C and shared high homologies among them and their counterparts circulated in other regions during the same period.