Genotyping and identification of non-polio enterovirus isolates from acute flaccid paralysis cases in Chongqing in 2013-2020 / 公共卫生与预防医学

Objective To classify and identify the 53 strains of non-polio enterovirus (NPEV) isolated from acute flaccid paralysis (AFP) cases in Chongqing from 2013 to 2020, and to investigate the genotype distribution of the strains. Methods Commercial real-time fluorescence quantitative polymerase chain reaction (real-time PCR) reagents were used for rapid identification of the strains. The nucleotide sequences of VP1 and VP4 regions were used for genotyping. Results Fifty enteroviruses were identified, 33 (66%) in group A and 17 (34%) in group B. Group C and D enteroviruses were not found in these strains，and 3 strains could not be identified. In this study, EV-A71 was the dominant type, with 11 strains (22%), but EV-A71 strain was not isolated since 2016. The sequences of VP4 region and VP1 region were completely consistent in enterovirus grouping. Conclusion When using commercial real-time PCR reagents for enterovirus typing, the identification results of high CT values may be inaccurate. In the genotyping of enterovirus, the nucleotide sequence of VP4 region is first used for grouping, and then the nucleotide sequence of VP1 region is used for genotyping, which could simplify the experimental process. NPEV isolates from AFP cases in Chongqing showed poor genotype diversity. In order to enrich and improve the enterovirus gene database in Chongqing, it is necessary to carry out research on enterovirus transmitted by respiratory tract.

Molecular epidemiological analysis on coxsackievirus B5 in certain areas of China / 中华实验和临床病毒学杂志

Objective@#To study the molecular epidemiology and genetic variation of coxsackievirus B5 (CV-B5) in certain areas in China.@*Methods@#MEGA 6.0 software was used to analyze the complete VP1 region of CV-B5 isolated strains from certain areas of China by retrieving the GenBank nucleotide database. Besides, the phylogenetic tree was constructed, the homology of nucleotide and amino acids were calculated and the rate of evolution was estimated.@*Results@#A total of 189 Chinese CV-B5 isolated strains were included in this study. Most of Chinese CV-B5 isolated strains belonged to genotype C, accounted for 90.5%. Compared with the genotype A, the homology of nucleotide sequences and amino acid sequences of complete VP1 region of 189 Chinese isolated strains were 79.8%-82.8% and 92.6%-97.9%, respectively; moreover, the nucleotide and the amino acid homology of 189 Chinese CV-B5 isolated strains among themselves ranged from 80.3% to 100.0% and ranged from 91.5% to 100.0%, respectively. The estimated rate of evolution of the CV-B5 was 4×10-3 substitutions/site/year.@*Conclusions@#The majority of CV-B5 isolated strains belonged to genotype C, and subgenotype C1 and C2 were co-circulating together in certain areas of China.

Real-time reverse transcription-polymerase chain reaction assays for identification of wild poliovirus 1 & 3.

Background & objectives: The poliovirus serotype identification and intratypic differentiation by real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay is suitable for serotype mixtures but not for intratypic mixtures of wild and vaccine poliovirus strains. This study was undertaken to develop wild poliovirus 1 and 3 (WPV1 and WPV3) specific rRT-PCR assays for use. Methods: Specific primers and probes for rRT-PCR were designed based on VP1 sequences of WPV1 and WPV3 isolated in India since 2000. The specificity of the rRT-PCR assays was evaluated using WPV1 and WPV3 of different genetic lineages, non-polio enteroviruses (NPEVs) and mixtures of wild/wild and wild/Sabin vaccine strains. The sensitivity of the assays was determined by testing serial 10-fold dilutions of wild poliovirus 1 and 3 stock suspensions of known titre. Results: No cross-reactivity with Sabin strains, intertypic wild poliovirus isolates or 27 types of NPEVs across all the four Enterovirus species was found for both the wild poliovirus 1 and 3 rRT-PCR assays. All WPV1 and WPV3 strains isolated since 2000 were successfully amplified. The rRT-PCR assays detected 104.40CCID50/ml of WPV1 and 104.00CCID50/ml of WPV3, respectively either as single isolate or mixture with Sabin vaccine strains or intertypic wild poliovirus. Interpretation & conclusions: rRT-PCR assays for WPV1 and WPV3 have been validated to detect all the genetic variations of the WPV1 and WPV3 isolated in India for the last decade. When used in combination with the current rRT-PCR assay testing was complete for confirmation of the presence of wild poliovirus in intratypic mixtures.