1.Genotyping of 90 autosomal SNPs based on next generation sequencing
Haiyan LI ; Chuchu ZHANG ; Zhenya TANG ; Ran LI ; Hongying CHEN ; Dayue TONG ; Hongyu SUN
Chinese Journal of Forensic Medicine 2016;31(6):557-562
Objective To investigate the genetic polymorphism of 90 autosomal SNPs in Guangdong Han population and assess their value in forensic medicine based on next generation sequencing. Methods Blood samples were collected from 100 unrelated individuals. Through using AutoMate ExpressTM Nucleic Acid Extraction System, DNA was extracted. HID-Ion AmpliSeq? Identity Panel was applied for library preparation while Ion OneTouch? 2 system (OT2) was employed for emulsion PCR (emPCR). NGS was performed on the Ion PGM? system. Sequencing results were analysed using the Torrent Suite v4.4.2 with the HID_SNP_Genotyper v4.3.1 plugin. The forensic parameters were calculated and compared with GoldeneyeTM 20A systems. Results According to the Bonferroni correction, the genotypes of 90 autosomal SNPs were in accordance with Hardy-Weinberg equilibrium and no linkage disequilibrium was observed. The average Ho of 90 autosomal SNPs was 0.423, the average DP was 0.560 and the average PIC was 0.329. The CDP (cumulative power of discrimination) of 90 autosomal SNPs system was 1-1.20×10-33, which was greater than that of 20A System. The CPEtri (cumulative excluding probability of trio paternity) was 0.999 999 911 and the CPEduo (cumulative excluding probability of duo paternity) was 0.999 882. Both of these two parameters were below that of 20A System. Conclusion It suggested that the 90 autosomal SNPs System can be applied to forensic individual discrimination and trio paternity testing independently. Besides, it is supposed to be used in the duo paternity testing as an assistant measure.
2.Full Sibling Identification by IBS Scoring Method and Establishment of the Query Table of Its Critical Value
Ran LI ; Chengtao LI ; Shumin ZHAO ; Haixia LI ; Li LI ; Riga WU ; Chuchu ZHANG ; Hongyu SUN
Journal of Forensic Medicine 2017;33(2):136-140,147
Objective T o establish a query table of IB S critical value and identification pow er for the detection system s w ith different num bers of ST R loci under different false judgm ent standards. Methods Sam ples of 267 pairs of full siblings and 360 pairs of unrelated individuals w ere collected and 19 auto-som al ST R loci w ere genotyped by G oldeneyeTM 20A system . T he full siblings w ere determ ined using IB S scoring m ethod according to the 'R egulation for biological full sibling testing'. T he critical values and identification pow er for the detection system s w ith different num bers of ST R loci under different false judgm ent standards w ere calculated by theoretical m ethods. Results A ccording to the form al IB S scoring criteria, the identification pow er of full siblings and unrelated individuals w as 0.7640 and the rate of false judgm ent w as 0. T he results of theoretical calculation w ere consistent w ith that of sam ple observation. T he query table of IB S critical value for identification of full sibling detection system s w ith different num bers of ST R loci w as successfully established. Conclusion T he IB S scoring m ethod defined by the regulation has high detection efficiency and low false judgm ent rate, w hich provides a relatively conservative result. T he query table of IB S critical value for identification of full sibling detection sys-tem s w ith different num bers of ST R loci provides an im portant reference data for the result judgm ent of full sibling testing and ow ns a considerable practical value.
3.Mutations in a Large Pedigree with Y-STR Genetic Markers
Shan PENG ; Chao LIU ; Ying WANG ; Yue LI ; Chuchu ZHANG ; Li HONG ; Xueling OU ; Hongyu SUN
Journal of Forensic Medicine 2015;(2):109-111,122
Objective To explore the mutation of Y-STR loci in meiotic allelic transmission in a large pedigree. Methods The oral swabs of 163 male individuals were collected froma L in pedigree. Twenty-two Y-STR genetic markers were typed with AGCUY 24 fluorescent detection kit (AGCUY 24 sys-tem), which also contained 16 Y-STR markers included in Y filerTmmultiple amplification kit (Y filer system). The genotyping results of Y-STR loci were compared between each two males in the pedigree. Results There were 20 and 30 kinds of haplotypes obtained with Y filer and AGCUY 24 systems in 163 male individuals fromthe L in pedigree, respectively. The rates referred to haplotype differences (RRHD) of these two typing systems between male pairs were 0.910 5 and 0.922 7, respectively. The average number of marker differences were 6.582 1 and 9.824 8, respectively. The RRHDincreased along with the incidents of meiosis. Conclusion Y-STR mutation leads to different Y-STR haplotypes among the male members in a paternal pedigree and the rate of difference increases along with the incidents of meiosis.
4.Tracing and transmission analysis of a nosocomial infection event caused by hypervirulent Acinetobacter baumannii
Chuchu LIN ; Min ZHANG ; Wenping ZHENG ; Wei HUANG
Chinese Journal of Clinical Infectious Diseases 2022;15(1):21-27
Objective:To trace and identify the source and the transmission vector of a nosocomial infection event caused by hypervirulent Acinetobacter baumannii. Methods:Nine strains of carbapenem-resistant Acinetobacter baumannii (CRAB) isolated from respiratory general ward and respiratory intensive care unit in Shenzhen People’s Hospital from July to August 2018 were collected. Environmental specimens such as ward environmental objects and medical staff’s hands were also collected. Vitek 2 was used for identification of bacterial species and drug susceptibility testing; Illuinam HiSeq 2500 platform, Staramr, Ridom SeqSphere+ were used for whole genome sequencing, drug resistance gene detection and multi-locus sequence typing (MLST); and IQ-Tree software, BEAST2 software package and SCOTTI software were used to construct phylogenetic tree and propagation path map. At the same time, the virulence of pathogenic bacteria was detected by mouse pneumonia model. Results:The 9 isolated CRAB strains were all ST2 type, all carried the carbapenem-resistant gene blaOXA-23, and the capsular types were KL49, KL3, KL77 and KL2, respectively. One of the CRAB strains isolated from removable ventilator screen was ST2 type and KL49 type capsule. Phylogenetic tree analysis showed that the environmental isolates were located in the same branch as 5 CRABs, and the transmission path map showed that these 5 CRABs were also located in the same transmission chain. Five strains of CRAB were involved in four lethal cases, and in vivo experiments in mice confirmed that the strains causing lethal infection had a hypervirulent phenotype. Conclusions:Highly virulent Acinetobacter baumannii can colonize the surface of mobile medical equipment, and sharing these equipment may lead to nosocomial spread of pathogens. The use of new propagation path analysis tools has certain reference significance for the investigation of propagation events.
5.Low disease activity and remission status of systemic lupus erythematosus in a real-world study
Limin REN ; Chuchu ZHAO ; Yi ZHAO ; Huiqiong ZHOU ; Liyun ZHANG ; Youlian WANG ; Lingxun SHEN ; Wenqiang FAN ; Yang LI ; Xiaomei LI ; Jibo WANG ; Yongjing CHENG ; Jiajing PENG ; Xiaozhen ZHAO ; Miao SHAO ; Ru LI
Journal of Peking University(Health Sciences) 2024;56(2):273-278
Objective:To investigate the rates of low disease activity and clinical remission in patients with systemic lupus erythematosus(SLE)in a real-world setting,and to analyze the related factors of low disease activity and clinical remission.Methods:One thousand patients with SLE were enrolled from 11 teaching hospitals.Demographic,clinical and laboratory data,as well as treatment regimes were collec-ted by self-completed questionnaire.The rates of low disease activity and remission were calculated based on the lupus low disease activity state(LLDAS)and definitions of remission in SLE(DORIS).Charac-teristics of patients with LLDAS and DORIS were analyzed.Multivariate Logistic regression analysis was used to evaluate the related factors of LLDAS and DORIS remission.Results:20.7%of patients met the criteria of LLDAS,while 10.4%of patients achieved remission defined by DORIS.Patients who met LLDAS or DORIS remission had significantly higher proportion of patients with high income and longer disease duration,compared with non-remission group.Moreover,the rates of anemia,creatinine eleva-tion,increased erythrocyte sedimentation rate(ESR)and hypoalbuminemia was significantly lower in the LLDAS or DORIS group than in the non-remission group.Patients who received hydroxychloroquine for more than 12 months or immunosuppressant therapy for no less than 6 months earned higher rates of LLDAS and DORIS remission.The results of Logistic regression analysis showed that increased ESR,positive anti-dsDNA antibodies,low level of complement(C3 and C4),proteinuria,low household in-come were negatively related with LLDAS and DORIS remission.However,hydroxychloroquine usage for longer than 12 months were positively related with LLDAS and DORIS remission.Conclusion:LLDAS and DORIS remission of SLE patients remain to be improved.Treatment-to-target strategy and standar-dized application of hydroxychloroquine and immunosuppressants in SLE are recommended.
6.The Prevention and Treatment of Pulmonary Nodules “Nodule-cancer Transformation” Based on the View of “Disease with Latent Pathogen Induced by a New Pathogen”
Yi LIU ; Chuchu ZHANG ; Bingyi YIN ; Qiyuan MAO ; Qianwen CHENG ; Ruijuan CAI ; Hongsheng LIN
Journal of Traditional Chinese Medicine 2024;65(1):39-43
As one of the pathogenic mechanisms contained in The Inner Canon of Yellow Emperor (《黄帝内经》), “disease with latent pathogen induced by a new pathogen” means that the induced new pathogen resulted to a combination of the latent previous pathogen and the new pathogen, which caused the disease. Based on this, it is believed that the change of “nodule-cancer transformation” of pulmonary nodules is actually based on the deficiency of original qi, and the new pathogen induces the latent pathogens like phlegm coagulation, qi stagnation, blood stasis, toxicity, so healthy qi can not drive the pathogens out, and the long-time detention generated into cancerous turbidity, and deve-loped into cancerous tumour at the end. Therefore, based on the three-stage treatment of unformed cancer, dense cancerous toxin, and developed cancer, the clinical practice applied six methods of clearing, expelling, dissipating, tonifying, harmonizing, and transforming, taking into account both the manifestation and root cause, moving the treatment window of pulmonary nodules forward, attacking the pathogens when the toxin was not yet overbearing, supporting the healthy qi before declining, delaying the process of nodules-cancer transformation, and providing ideas for the prevention and treatment of pulmonary nodules “nodule-cancer transformation” in traditional Chinese medicine.
7.Analysis of epidemiological characteristics of the clustered cases of hand, foot and mouth disease in Pudong New Area, Shanghai, 2017‒2022
Jiafeng CHEN ; Anran ZHANG ; Hongmei XU ; Huozheng GU ; Chuchu YE ; Yuanping WANG
Shanghai Journal of Preventive Medicine 2024;36(5):439-443
ObjectiveTo analyze the epidemiological characteristics and etiology of clustered outbreaks of hand, foot, and mouth disease (HFMD) in Pudong New Area, Shanghai from 2017 to 2022, and to provide a scientific basis for the prevention and control of HFMD in the area. MethodsThe data related to HFMD clustered outbreaks from 2017 to 2022 were obtained from the Pudong New Area HFMD outbreak database. Descriptive analysis was conducted to explore the outbreak scope, seasonal characteristics, distribution of occurrence settings, and etiological composition. ResultsFrom 2017 to 2022, Pudong New Area reported a total of 2 547 HFMD clusters, involving 8 884 cases, with an average of 3.49 cases per event. The majority of events (78.52%) had between 2 and 4 cases. The peak reporting periods for clustered HFMD from 2017 to 2019 and in 2021 were during the summer (May‒July) and autumn (September‒November). The seasonal pattern was less distinct in 2020 and 2022, likely due to the impact of the COVID-19 pandemic. The majority of clustered outbreaks occurred in childcare facilities (44.64%), followed by households/neighborhood committees (44.21%), with schools accounting for a smaller proportion (12.39%). The etiology revealed the coexistence of multiple enterovirus genotypes, with a positive detection rate of 60.46%, and CoxA6 being the dominant strain. ConclusionHFMD clustered outbreaks in Pudong New Area show fluctuating trends, with significant yearly differences in the number of incidents. The predominant seasons for outbreaks are summer and autumn, with CoxA6 identified as the dominant strain. The implementation of prevention and control measures for COVID-19 significantly reduced the occurrence of HFMD outbreaks. Continuous monitoring and focus on large-scale clustered outbreaks in key institutions are essential for the future.
8.Herbal Textual Research on Polygonati Odorati Rhizoma in Famous Classical Formulas
Xue LI ; Cunde MA ; Chuchu ZHANG ; Sihong LIU ; Huamin ZHANG ; Bing LI ; Zhilai ZHAN
Chinese Journal of Experimental Traditional Medical Formulae 2023;29(12):13-25
This article has systematically reviewed the name, origin, scientific name, producing area, quality evaluation, harvesting and processing methods of Polygonati Odorati Rhizoma(POR) by consulting the materia medica, medical books, prescription books and modern literature, in order to provide a reference for the development of famous classical formulas containing POR. Yuzhu was first recorded in the Shennong Bencaojing under the name of Nyuwei. After that, Weirui was used as the rectification name in the subsequent dynasties, and in recent times, the name of Yuzhu is mostly used in materia medica and prescription books. In ancient times, there were different names for Yuzhu, such as Nyuwei, Weiwei and Weirui. The names of the three are similar and there was a mixed use of the same name and foreign matter in history. In the Tang dynasty, SU Jing listed Nyuwei with the effect of curing dysentery in the intermediate of herbal part of Xinxiu Bencao according to its different efficacy. However, based on Shennong Bencaojing, Mingyi Bielu and the different energy efficiency of medical prescriptions, SU Song of the Northern Song dynasty believed that the three were medicinal materials of different origins. In short, the names of the three have been unclear in history for a long time. According to the development of the time line, this paper examines the names and realities of the three, and concludes that the two(Weiwei and Weirui) are the same medicinal material, that is, Polygonatum odoratum of Liliaceae, and the Nyuwei is Clematis apiifolia of Ranunculaceae, and the source relationship of the three is clarified. The mainstream source of Yuzhu used in the past dynasties was the rhizome of P. odoratum, which was widely distributed in the wild and has a large amount of resources. The origins of Yuzhu recorded in ancient times were mainly Taishan in Shandong, Chuzhou and Shuzhou in Anhui, and Hanzhong in Shaanxi, in modern times, it was produced in northern Hebei and Shaoyang in Hunan with high quality, and in the modern times, Jiangbei Yuzhu from Haimen in Jiangsu, Anyuzhu from Nanling, Anqing and Tongling in Anhui, Guanyuzhu from Fengrun, Yutian, Zunhua, Huailai in Hebei and Suizhong, Jinxi, Jianchang, Lingyuan, Liaoyang, Haicheng, Gaiping in Liaoning, Xiangyuzhu from Shaoyang in Hunan are the authentic medicinal material. In ancient times, the quality of Yuzhu was good if it was fat and white, while in modern times, it is better with thick roots, bright yellow color, soft texture, no stiff skin and no oiliness. In ancient times, the origin processing of POR was mostly dried in the shade, but in modern times, it is mostly sun-dried or dried after steaming and rubbing. The ancient processing was mostly scraped off the skin and soaked in honey water and then steamed through, while the modern one is mostly washed and cut into thick slices for raw use. Based on the conclusion of the herbal textual research, it is suggested that the rhizome of P. odoratum of Liliaceae be used as the source for the development of famous classical formulas, and the corresponding specifications be selected according to the processing requirements of the prescription. In view of the Yiweitang in Wenbing Tiaobian, which uses the method of frying fragrance to achieve the effect of fragrant refreshing the spleen, it can be processed by referring to the stir-frying method in the current version of Chinese Pharmacopoeia.
9.Analysis of cases of reinfection of past SARS-CoV-2 patients in Pudong New Area of Shanghai
Ge ZHANG ; Anran ZHANG ; Yilin JIA ; Li ZHANG ; Lipeng HAO ; Hongmei XU ; Yuanping WANG ; Chuchu YE ; Bo LIU ; Weiping ZHU ; Yixin ZHOU
Shanghai Journal of Preventive Medicine 2024;36(2):117-122
ObjectiveTo identify the rate, population characteristics, and vaccination history of repeat infections among previously infected people in the current epidemic based on the rate of repeat infection and population characteristics of different mutant strains at different times in Pudong New Area of Shanghai, and to provide reference for the prevention and control strategies of novel coronavirus repeat infections. MethodsA total of 9 250 investigated subjects were randomly selected from the new cases of asymptomatic infection and confirmed cases reported by Pudong New Area from March to May 2022. The investigation mainly focused on demographic characteristics, nucleic acid or antigen test results, and symptoms after infection. The repeat infection rates among different populations were compared, and logistic regression was used to analyze the impact of gender, age, and vaccination status on repeat infections. ResultsThe survey sample of 9 250 people had a response rate of 81.85%. There were 4 043 males (53.40%) and 3 528 females (46.60%), with a median age of 34 years old (P25, P75: 7, 61). The overall vaccine uptake rate was 59.44% (4 500/7 571). In December of 2022, there were 563 cases of repeat infection, with an infection rate of 7.44%. The lowest rate of repeat infection was seen in the 3‒ year-old group (2.86%) and the highest rate in the 30‒ year-old group (12.42%), with significant differences between different age groups. The repeated infection rate for those who had completed their vaccinations was significantly lower (6.57%) compared to those who had not (7.11%). The age groups of 3‒ years, 70‒79 years, as well as individuals who completed full vaccination and received booster shots were protective factors against repeat infections. ConclusionThe overall rate of reinfection among the infected in Shanghai during the spring of 2022 was low in the outbreak of the Omicron variant, and the rate of reinfection in the 3‒ year-old group was significantly lower than in other age groups. Completing the full course of vaccination significantly reduces the risk of reinfection. Although the reinfection rate is high in individuals who received booster shots, it remains a mitigating factor compared to those who do not receive the vaccine. It is recommended to continue monitoring reinfections in key populations and further strengthen immunization efforts.
10.Virus spectrum of inpatients with acute respiratory infection in Pudong New Area , Shanghai
Zou CHEN ; Dan LIU ; Chuchu YE ; Hong ZHANG ; Qi ZHAO ; Lipeng HAO
Journal of Public Health and Preventive Medicine 2024;35(2):21-24
Objective To understand the viral spectrum of inpatients with acute respiratory infection in Pudong New Area, and to explore the composition of pathogens in hospitalized children and adults. Methods Samples of acute respiratory infection cases from 10 medical institutions were collected from 2011 to 2020 and tested for human influenza virus, human adenovirus, rhinovirus, human parainfluenza virus, respiratory syncytial virus, human coronavirus, human metapneumovirus and human boca virus. Results A total of 3 145 inpatients were monitored, with a median age of 61 years. The positive rate of any virus was 32.43% (1 020/3 145), and the single virus infection accounted for 85.98% (877/1 020). In single virus infection, the positive rate of human influenza virus was the highest (9.67%, 304/3 145), with influenza A (80.26%, 244/304) as the main virus. The second was rhinovirus (3.97%, 125/3 145). The positive rate of any virus in different age groups was statistically significant (χ2=103.38,P<0.001). The positive rate of respiratory syncytial virus was the highest in the ~5-year-old group, adenovirus was the highest in the 6-14-year-old group, and influenza virus was the highest in the 15-64-year-old group and the 65year-old group. There was a significant difference in the positive rate of any virus in each month (χ2=123.06,P<0.001). The human influenza virus was the dominant virus in winter (December to February) and summer (July to September), and rhinoviruses distributed sporadically in each month. The positive rate of any virus in different departments was significantly different (χ2=90.37,P<0.001). Conclusion The positive rate of virus in hospitalized patients with acute respiratory infection is relatively high in Pudong New Area, Shanghai, with human influenza virus being the main virus. The virus spectrum of hospitalized children and adults is inconsistent. In the future, in-depth research should be strengthened, focusing on the distribution of pathogens in different populations and seasonal prevention and treatment.