Objective:To understand the epidemiological characteristics and spatiotemporal distribution of viral encephalitis in children and adolescents in Henan Province from 2012 to 2023.Methods:The information about viral encephalitis cases from October 1, 2012 to July 26, 2023 were collected from Zhengzhou Children's Hospital (National Children's Regional Medical Center),Henan Provincial Children's Hospital for the analyses on temporal distribution the cases, the severe illness rate, age distribution, pathogen type and imaging findings of the cases.Results:A total of 6 276 cases of viral encephalitis were included in this study after excluding cases with incomplete information. The cases mainly originated from Zhengzhou (38.96%), followed by Zhoukou (9.93%), Xuchang (8.68%), Zhumadian (7.90%) and Pingdingshan (7.39%). The cases in boys accounted for 62.13% and the cases in girls accounted for 37.87%. Most cases (72.45%) occurred in age group 7-13 years. The overall rate of severe illness cases was 4.51% from 2012 to 2023. There were significant differences in severe illness cases among different areas and years ( χ2=5.33, P=0.021; χ2=48.14, P<0.001). Enteroviruses were mainly detected (31.57%), in which Coxsackie virus was predominant (58.37%). Imaging findings showed that cerebral hemisphere damage was most common in children and adolescents with viral encephalitis (54.93%). Conclusions:From 2012 to 2023, more cases of viral encephalitis occurred in boys in Henan. Children and adolescents aged 7-13 years were the main affected group. The prevention of enteroviruses infection, especially Coxsackie virus, needs to be strengthened. Special attention should be paid to the prevention of cerebral hemisphere damage after viral encephalitis diagnosis.

Objective: To evaluate the typing and clinical application effect based on clustered regularly interspaced short palindromic repeats (CRISPRs), serotype, and Multilocus Sequence Typing (MLST). Methods: The spacers, serotype and sequence type (ST) were obtained with CRISPRsFinder, SeroTypeFinder and MLST. PCR was used to amplify the CRISPRs, and the spacers were used to predict serotype and ST, then comparing with the serotype and ST. Results: We defined the I-E CRISPR/Cas as CT-Ⅰ, I-F CRISPR/Cas as CT-Ⅱ, and only CRISPR3-4 as CT-Ⅲ. We designated each unique arrangement spacer profile as a unique CRISPRs type. A total of 79 CT types, 76 serotypes, and 66 STs were identified. The CRISPRs typing was the most discriminating, with the Simpson index of 0.936, having the highest correlation with serology with the adjusted Rand index of 0.908. The CRISPRs type could divide the same serotype (ST) into two subtypes [O157∶H7(ST11), O104∶H4(ST678), and O26∶H11(ST21)]. The detection rates of CRISPR1, CRISPR2, CRISPR3, CRISPR4, and CRISPR3-4 were 81.1%, 94.5%, 1.4%, 1.4%, and 4.6%, with the accuracy rate of 95.0% and 100.0% according to the spacers to forecast O157∶H7 (ST11) and ST131. Conclusion: Based on the CRISPRs spacer, this method can be used as an essential molecular typing for E.coli, as it presents a good typing and clinical application effect.
Escherichia coli/genetics* ; Escherichia coli Infections ; Humans ; Multilocus Sequence Typing

Objective:To establish a rapid detection method for human astrovirus based on TaqMan-probe real-time fluorescent quantitative reverse transcription-polymerase chain reaction (RT-PCR).Methods:According to the conservative sequence of human astrovirus ORF1 b gene, we designed the amplification primers and specific fluorescent probe to establish the human astrovirus TaqMan real-time fluorescent quantitative RT-PCR rapid detection method. The specificity, sensitivity and stability of the method were evaluated. We also used this method to detect human astrovirus in clinical samples. Results:The established human astrovirus TaqMan real-time fluorescent quantitative RT-PCR detection method has good specificity and repeatability for human astrovirus, and the sensitivity can reach 10 2 copies/μl. After testing the clinical samples, the detection rate of human astrovirus by our method was 100%. Conclusions:The human astrovirus TaqMan real-time fluorescent quantitative RT-PCR detection method established in this study is simple, rapid, sensitive, specific and stable. It can be used for clinical human astrovirus detection and epidemiological investigation.

Since December 2019, Corona Virus Disease (COVID-19), a new emerging infection disease occurred in Wuhan, has spread in 27 countries and regions. The clusters of many cases were reported with the epidemic progresses. We collected currently available information for 377 COVID-19 clusters (1 719 cases), excluded the hospital clusters and Hubei cases, during the period from January 1, 2020 to February 20, 2020. There were 297 family clusters (79%), case median 4; 39 clusters of dining (10%), case median 5; 23 clusters of shopping malls or supermarkets (6%), case median 13; 12 clusters of work units (3%), case median 6, and 6 clusters of transportation. We selected 325 cases to estimate the incubation period and found its range is 1 to 20 days, median was 7 days, and mode was 4 days. The analysis of the epidemic situation in a department store in China indicates that there is a possibility of patients as the source of infection during the incubation period of the epidemic. From February 5, 2020 to February 21, 2020, 634 persons were infected in the Diamond Princess Liner. All persons are susceptible to SARS-CoV-2. The older, patients during the incubation period and the worse environment may be the cause of the cases rising. The progress of the two typical outbreaks clearly demonstrates the spread of the early cases in Wuhan. Whatever happens, screening and isolating close contacts remains essential except for clinical treatment during the epidemic. Especially for the healthy people in the epidemic area, isolation is the key.

Objective:To analyze the characteristics of COVID-19 case spectrum and spread intensity in different provinces in China except Hubei province.Methods:The daily incidence data and case information of COVID-19 were collected from the official websites of provincial and municipal health commissions. The morbidity rate, severity rate, case-fatality rate, and spread ratio of COVID-19 were calculated.Results:As of 20 March, 2020, a total of 12 941 cases of COVID-19 had been conformed, including 116 deaths, and the average morbidity rate, severity rate and case-fatality rate were 0.97/100 000, 13.5 % and 0.90 %, respectively. The morbidity rates in Zhejiang (2.12/100 000), Jiangxi (2.01/100 000) and Beijing (1.93/100 000) ranked top three. The characteristics of COVID-19 case spectrum varied from province to province. The first three provinces (autonomous region, municipality) with high severity rates were Tianjin (45.6 %), Xinjiang (35.5 %) and Heilongjiang (29.5 %). The case-fatality rate was highest in Xinjiang (3.95 %), followed by Hainan (3.57 %) and Heilongjiang (2.70 %). The average spread ratio was 0.98 and the spread intensity varied from province to province. Tibet had the lowest spread ratio (0), followed by Qinghai (0.20) and Guangdong (0.23). Conclusion:The intervention measures were effective in preventing the spread of COVID-19 and improved treatment effect in China. However, there were significant differences among different regions in severity, case-fatality rate and spread ratio.

Objective To explore the stability of resistant phenotypes and changes of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) gene system on four Shigella strains in the absence of antibiotics.Methods Four clinical isolated Shigella strains that resistant to different antibiotics were consecutive passaged for 90 times without antibiotics.Agar dilution method was used to determine the minimum inhibitory concentration of Shigella strains.After sequence analysis with PCR,CRISPR Finder and Clustal X 2.1 were applied to identify the changes of CRISPR loci in the Shigella strains.Results After the consecutive transfer of 90 generations,sensitivity to certain antibiotics of four Shigella strains with different drug resistant spectrums increased.Mel-sf1998024/zz resistance to ampicillin,cephalexin,cefotaxime,chloramphenicol decreased,mel-s2014026/sx resistance to norfloxacin,trimethoprim decreased,mel-sf2004004/sx drug resistance to ampicillin,cefuroxime,cefotaxime,chloramphenicol,trimethoprim decreased and mel-sf2013004/bj resistance to chloramphenicol decreased.The spacer of which matched gene codes Cas and its upstream repeat in 3'end of CRISPR3 got lost in mel-sf1998024/zz and mel-sf2013004/bj.Conclusions Shigella strains could reduce or lose their resistance to some antibiotics after consecutive transfers,without the interference of antibiotics.CRISPR3 locus had dynamic spacers in Shigella strains while CRISPR3 locus and cas genes might have been co-evolved.

Objective To investigate the association between phage-mediated shiga toxin and molecular distribution of CRISPR in Escherichia (E.) coli O26:H11 or NM.Methods A total of 135 E.coli O26:H11 or NM strains were collected from NCBI database.Software CRT and CRISPR Finder were used to extract CRISPR and Excel was used to assign the spacer of unique number and type CRISPR.And the relationship between CRISPR and stx phage was analyzed.Results All the 135 E.coli O26:H11 or NM strains had the CRISPR.For CRISPRI,CRISPR2.1,CRISPR2.2 and CRISPR3-4,19,22,1 and 1 subtypes were found,respectively.According to the four CRISPR sites,the strains could be divided into 40 subtypes.Stx-phage was only observed in the group C of CRISPR.Compared with E.coli of stx-phage negative,E.coli with stx-phage harbored more spacers.Conclusions CRISPR loci was extensively existed in E.coli O26:H11 or NM,and many subtypes were found in these strains.The presence of stx-phage was related to the molecular distribution of CRISPR in E.coli O26:H11 or NM.CRISPR might be a valuable biomarker to identify strains with high virulent potential.

Molecular epidemiology,a branch of epidemiology,combines the theories and methods,both in epidemiology and molecular biology.Molecular epidemiology mainly focuses on biological markers,describing the distribution,occurrence,development and prognosis of diseases at the molecular level.The completion of Human Genome Project and rapid development of Precision Medicine and Big Data not only offer the new development opportunities but also bring about a higher demand and new challenge for molecular epidemiology.

This study was aimed to explore the features of clustered regularly interspaced short palindromic repeats (CRISPR) structures in Shigella by using bioinformatics. We used bioinformatics methods, including BLAST, alignment and RNA structure prediction, to analyze the CRISPR structures of Shigella genomes. The results showed that the CRISPRs existed in the four groups of Shigella, and the flanking sequences of upstream CRISPRs could be classified into the same group with those of the downstream. We also found some relatively conserved palindromic motifs in the leader sequences. Repeat sequences had the same group with corresponding flanking sequences, and could be classified into two different types by their RNA secondary structures, which contain "stem" and "ring". Some spacers were found to homologize with part sequences of plasmids or phages. The study indicated that there were correlations between repeat sequences and flanking sequences, and the repeats might act as a kind of recognition mechanism to mediate the interaction between foreign genetic elements and Cas proteins.
Base Sequence ; Clustered Regularly Interspaced Short Palindromic Repeats ; Computational Biology ; Genome, Bacterial ; Plasmids ; Shigella ; genetics

Objective To investigate the dynamic changes in the serum inflammatory cytokines and their association with neurogenic pulmonary edema (NPE) in the patients with severe hand-foot-mouth disease (HFMD).Methods Eighty-nine patients with severe HFMD from March 2010 to December 2012 were recruited in the study.The patients were divided into NPE group and central nervous system diseases (CNSD) group according whether they had NPE.The cytokines,including interleukin (IL)-4,IL-6,IL-10,IL-17,tumor necrosis factor-α (TNF-α) and interferon-γ(IFN-γ)were evaluated by using enzyme-linked immunosorbent assay on day 1,3 and 5 after admission to hospital.Risk factors for NPE involvement during hospital stay were analyzed with multivariate Logistic regression analysis.Results (1) Compared with the CNSD group,the serum levels of IL-6 (Ftime =1.876,P =0.177,Ftime* group =2.192,P =0.145,Fgroup =7.855,P =0.007),TNF-α(Ftime =13.133,P =0.001,Ftime* group =0.291,P =0.592,Fgroup =3.644,P =0.042),IL-10 (Ftime =14.580,P =0.001,Ftime* group =2.612,P =0.078,Fgroup =16.823,P =0.000),INF-γ (Ftime =3.093,P =0.045,Ftime* group =0.513,P =0.600,Fgroup =20.141,P =0.000) were significantly higher than those in NPE group.(2)The serum levels of TNF-α,IL-10,INF-γ rose to the peak on the third day.(3) By using multivariate Logistic regression analysis,age (OR =3.383,95％ CI:1.173-4.759),days of fever (OR =4.925,95％ CI:1.758-3.794),hyperglycaemia (OR =3.465,95％ CI:1.303-5.220),leucocytosis (OR =7.579,95 ％ CI:2.530-12.704) and elevation of IL-10 (OR =1.228,95 ％ CI:1.007-1.523) were entered into equation.In the risk evaluation model,these variables remained independent predictors for NPE.Conclusions Abnormal cytokine productions appear to be responsible for the pathogenesis of NPE,and might be an effective tool for predicting NPE in infants with severe HFMD.