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A unified global genotyping framework of dengue virus serotype-1 for a stratified coordinated surveillance strategy of dengue epidemics

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infectious diseases of Poverty 2022年第5期11卷 14-29页

作者： Liqiang Li Xiang Guo Xiaoqing Zhang Lingzhai Zhao Li Li Yuji Wang Tian Xie Qingqing Yin Qinlong Jing Tian Hu Ziyao Li Rangke Wu Wei Zhao Sherman Xuegang Xin Benyun Shi Jiming Liu Shang Xia Zhiqiang Peng Zhicong Yang Fuchun Zhang Xiao‑Guang Chen Xiaohong Zhou Institute of Tropical Medicine Southern Medical UniversityGuang‑zhou 510515China Key Laboratory of Prevention and control for Emerging infectious diseases of Guangdong Higher Institutes Guangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Pathogen BiologySchool of Public HealthSouthern Medical UniversityGuangzhou 510515China Institute of infectious diseases Guangzhou Eighth People’s HospitalGuangzhou Medical UniversityGuangzhou 510060GuangdongChina State Key Laboratory of Organ Failure Research Guangdong Provincial Key Labora‑tory of Tropical Disease ResearchDepartment of BiostatisticsSchool of Public HealthSouthern Medical UniversityGuangzhou 510515China Guangzhou Center for disease control and Prevention Guangzhou 510440China School of Foreign Studies Southern Medical UniversityGuangzhou 510515China BSL‑3 Laboratory(Guangdong) School of Public HealthSouthern Medical UniversityGuangzhou 510515China Laboratory of Biophysics School of MedicineSouth China University of TechnologyGuangzhou 510006China School of Computer Science and Technology Nanjing Tech UniversityNan‑jing 211816China Department of Computer Science Hong Kong Baptist UniversityKowloonHong Kong 999077China National Institute of Parasitic diseases at Chinese Center for disease control and Prevention(Chinese Center for Tropical diseases Research) NHC Key Laboratory of Parasite and Vector BiologyWHO Collaborating Centre for Tropical DiseasesShanghaiPeople’s Republic of China School of Global Health Chinese Center for Tropi‑cal Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai 200025China Guangdong Provincial Center for disease control and Prevention Guangzhou 511430China

Background: Dengue is the fastest spreading arboviral disease, posing great challenges on global public health. A reproduceable and comparable global genotyping framework for contextualizing spatiotemporal epidemiological data of dengue virus (DENV) is essential for research studies and collaborative ***: Targeting DENV-1 spreading prominently in recent decades, by reconciling all qualified complete E gene sequences of 5003 DENV-1 strains with epidemiological information from 78 epidemic countries/areas ranging from 1944 to 2018, we established and characterized a unified global high-resolution genotyping framework using phylogenetics, population genetics, phylogeography, and ***: The defined framework was discriminated with three hierarchical layers of genotype, subgenotype and clade with respective mean pairwise distances 2-6%, 0.8-2%, and ≤ 0.8%. The global epidemic patterns of DENV-1 showed strong geographic constraints representing stratified spatial-genetic epidemic pairs of Continent-Genotype, Region-Subgenotype and Nation-Clade, thereby identifying 12 epidemic regions which prospectively facilitates the region-based coordination. The increasing cross-transmission trends were also demonstrated. The traditional endemic countries such as Thailand, Vietnam and Indonesia displayed as persisting dominant source centers, while the emerging epidemic countries such as China, Australia, and the USA, where dengue outbreaks were frequently triggered by importation, showed a growing trend of DENV-1 diffusion. The probably hidden epidemics were found especially in Africa and India. Then, our framework can be utilized in an accurate stratified coordinated surveillance based on the defined viral population compositions. Thereby it is prospectively valuable for further hampering the ongoing transition process of epidemic to endemic, addressing the issue of inadequate monitoring, and warning us to be concerned about the cross-national, cross

关键词： Dengue virus serotype-1(DENV-1) Molecular epidemiology Population structure Phylogeography Global genotyping framework Molecular surveillance

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Identification of the high-risk area for schistosomiasis transmission in China based on information value and machine learning:a newly data-driven modeling attempt

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infectious diseases of Poverty 2021年第3期10卷 113-114页

作者： Yan-Feng Gong Ling-Qian Zhu Yin-Long Li Li-Juan Zhang Jing-Bo Xue Shang Xia Shan Lv Jing Xu Shi-Zhu Li National Institute of Parasitic diseases Chinese Center for Disease Control and PreventionChinese Center for Tropical Diseases ResearchHC Key Laboratory of Parasite and Vector BiologyWHO Collaborating Centre for Tropical DiseasesNational Center for International Research on Tropical DiseasesShanghai 200025China

Background:Schistosomiasis control is striving forward to transmission interruption and even elimination,evidence-lead control is of vital importance to eliminate the hidden dan gers of *** study attempts to ide ntify... 详细信息

关键词： Schistosomiasis Risk prediction Information value Machine learning China

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Stepwise prediction and statistical screening:B-cell epitopes on neuraminidase of human avian H_5N_1 virus

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Chinese Science Bulletin 2008年第23期53卷 3642-3647页

作者： HUANG Ping YU ShouYi KE ChangWen Key Laboratory for Emergency Pathogen Detection Center for Disease Control and Prevention of Guangdong Province Guang- zhou 510300 China Department of epidemiology Southern Medical University Guangzhou 510515 China collaborating Center for Surveillance Research and Training of Emerging infectious Diseases World Health Organization Guangzhou 510300 China

The B-cell epitopes of virus are associated with the antiviral drug and the vaccine screening. As the nucleotide sequences of neuraminidase (NA) of stain GD-01-06 were sequenced, we predicted the α-helix and β-fold structure and the indexes of the flexible regions of secondary structure of NA with methods of the Hydrophilicity plot by Kyte-Doolittle, the Surface probability plot by Emini and the Antigenic index by Jameson-Wolf, and then screened statistically the parameters to predict B-cell epitopes by the Hierarchical cluster and the Bivariate correlation and the quartiles with SPSS 13.0. The impact of variation of amino acids in NA on its epitopes was analyzed. The predictive results were evaluated by Wu’s Antigenic Index and SWISS-MODEL. We found that the most possible epitopes on NA were located within or nearby its N-terminal Nos. 120―137, 81―84, 408―415, 273―282, 429―432, 356―368, 46―55, 146―155, 341―350 and 198―209, which were the dominant regions of NA epitopes. Peptide 120―137 including the glycoprotein domain (NGT126―128) was first chosen as the B-cell epitopes on NA. NA in H5N1 strain isolated after 2003 lacked in No. 53 amino acid (I), resulting in an increase in the surface flexible region of NA in GD-01-06 and an enlargement to their epitope regions (VEP46―48→ VEPISNTNFL46―55). Conclusively, prediction of the B-cell epitopes on the NA based on multiple parameters is useful for researches on the molecular immunology and drug screening and immuno-prophylaxis. A deletion of No. 53 amino acid (I) in NA in strain GD-01-06 might increase its antigenicity.

关键词：唾液酸苷酶人体 H5N1病毒细胞

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National Alveolar Echinococcosis Distribution--China, 2012−2016

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China CDC weekly 2020年第1期2卷 1-7页

作者： Canjun Zheng Chuizhao Xue Shuai Han Zhongjie Li Hu Wang Liying Wang Ying Wang Qian Wang Yu Feng Yanyan Hou Xiao Ma Junying Ma Xiumin Han Gongsang Quzhen Xiaofeng Jiang Weidong Guo Xianglin Wu Yaming Yang Lei Cao Fanka Li Weiqi Chen Xinliu Yan Shicheng Yu Meihua Fu Qing Yu Ning Xiao Jiangping Cao Jun Yan Weiping Wu Xiao-nong Zhou Division of infectious diseases Chinese Center for Disease Control and PreventionBeijingChina National Institute of Parasitic diseases Chinese Center for Disease Control and PreventionChinese Center for Tropical Diseases ResearchWHO Collaborating Centre for Tropical DiseasesNational Center for International Research on Tropical DiseasesMinistry of Science and TechnologyKey Laboratory of Parasite and Vector BiologyMinistry of HealthShanghaiChina Health Commission of Qinghai Province XiningQinghaiChina Sichuan Provincial Center for disease control and Prevention ChengduSichuanChina Gansu Provincial Center for disease control and Prevention LanzhouGansuChina Xingjiang Uyghur Autonomous Region Center for disease control and Prevention UrumqiXinjiangChina Qinhai Institute for Endemic disease Prevention and control XiningQinghaiChina Qinghai Provincial People’s Hospital XiningQinghaiChina Tibet Center for diseases control and Prevention LhasaTibetChina Inner Mongolia Autonomous Region Center for diseases control and Prevention HohhotInner MongoliaChina Ningxia Center for disease control and Prevention YinchuanNingxiaChina Yunnan Institute of Parasitic diseases PuerYunnanChina Shaanxi Provincial Center for disease control and Prevention Xi’anShaanxiChina Xinjiang Production and Construction Corps Center for disease control and Prevention UrumqiXinjiangChina Henan Provincial Center for disease control and Prevention ZhengzhouHenanChina Office of epidemiology Chinese Center for Disease Control and PreventionBeijingChina National Health Commission of the People’s Republic of China BeijingChina.

What is already known about this topic?Both alveolar echinococcosis(AE)and cystic echinococcosis are endemic in China,among which alveolar echinococcosis has a very high mortality *** is added by this report?The survey results showed the prevalence and scope of AE in China and identified high-risk groups including children,monks,herdsmen and illiterate *** the same time,all the cases found in the survey(more than 90%of the patients did not go to the hospital for diagnosis and treatment before survey)were promptly diagnosed and *** are the implications for public health practice?This study provides information for the development of a plan for AE prevention and control and for the implementation of interventions targeted to high-risk populations.

关键词： prevention diagnosis mortality

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Wastewater surveillance and an automated robot:effectively tracking SARS-CoV-2 transmission in the post-epidemic era

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National Science Review 2023年第6期10卷 86-95页

作者： Guanyong Ou Yuxuan Tang Shiyu Niu Liwen Wu Shaxi Li Yang Yang Jun Wang Yun Peng Chuanfu Huang Wei Hu Qinghua Hu Yinghui Li Yang Ping Chao Lin Boping Yu Qi Han Yabin Hao Zhiguang Luo Wende Tian Han Zhang Yingxia Liu School of Civil and Environmental Engineering Harbin Institute of Technology (Shenzhen) 1Institute of Solid Wastes and Physical Environment Research Shenzhen Academy of Environmental Sciences Shenzhen Metasensing Technology Co. Ltd. 13. Zhongmin (Shenzhen) intelligent ecology Co. Ltd. Research centre for Eco-Environmental Sciences Chinese Academy of Sciences National Clinical Research Center for infectious disease State Key Discipline of Infectious Disease The Third People's Hospital of Shenzhen Second Hospital Affiliated to Southern University of Science and Technology School of Medicine Southern University of Science and Technology International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education Institute of Microscale Optoelectronics College of Physics and Optoelectronic Engineering Shenzhen University Shenzhen Longhua Drainage Co. Ltd. Shenzhen Center for disease control and Prevention Microbiology Laboratory Shenzhen Center for Disease Control and Prevention Power China Eco-Environmental Group Co. Ltd. Shenzhen Water Planning & Design Institute Co. Ltd. Shenzhen Academy of Environmental Sciences

Wastewater-based epidemiology(WBE) has exhibited great utility in the early and rapid identification of SARS-C ***,the efficacy of wastewater surveillance under China’ s previous strict epidemic prevention policy remains to be *** collected the WBE data of wastewater treatment plants(WWTPs) in the Third People’s Hospital of Shenzhen and several communities to determine the significant effectiveness of routine wastewater surveillance in monitoring the local spread of SARS-C oV-2under tight containment of the *** results of 1 month of continuous wastewater surveillance showed that positive signals for SARS-C oV-2 RNA were detected in the wastewater samples,and a significant positive correlation was observed between the virus concentration and the number of daily *** addition,the community’ s domestic wastewater surveillance results were confirmed even 3 days before,or simultaneously with,the infected patient being confirmed as having the ***,an automated sewage virus detection robot,ShenNong No.l robot,was developed,showing a high degree of agreement with experimental data,offering the possibility of large-scale multi-point ***,our results illustrated the clear indicative role of wastewater surveillance in combating COVID-19 and provided a practical basis for rapidly expanding the feasibility and value of routine wastewater surveillance for future emerging infectious diseases.

关键词： SARS-CoV-2 wastewater surveillance wastewater-based epidemiology WWTP automated robot

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Cost-effectiveness analysis of the integrated control strategy for schistosomiasis japonica in a lake region of China: a case study

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infectious diseases of Poverty 2021年第3期10卷 109-110页

作者： Ling-Ling Wu He-Hua Hu Xia Zhang Xiao-Nong Zhou Tie-Wu Jia Can Wang Zhong Hon Jing Xu Nation al Institute of Parasitic diseases Chinese Center for Disease Control and PreventionChinese Center for Tropical Diseases ResearchNHC Key Laboratory of Parasite and Vector BiologyWHO Collaborating Centre for Tropical DiseasesNational Center for International Research On Tropical DiseasesShanghai 200025China 不详

Background:Schistosomiasis japonica remains an important public health concern due to its potential to cause severe outcomes and Iong-term *** integrated control strategy implemented in the Peoples' Republic of China has been shown to be effective to control or interrupt the transmission of *** objective of this study is to estimate the disease burden of schistosomiasis and assess the cost-effectiveness of the integrated control strategy focused on different major interventions at three stages for schistosomiasis control in a lake setting,to provide reference for policy making or planning.

关键词： Schistosomiasis Integrated control Cost-effectiveness Disability-adjusted life years China

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A relatively high zoonotic trematode prevalence in Orientogalba ollula and the developmental characteristics of isolated trematodes by experimental infection in the animal model

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infectious diseases of Poverty 2022年第4期11卷 72-80页

作者： Jian Li Yijing Ren Lei Yang Jiani Guo Haiying Chen Jiani Liu Haoqiang Tian Qingan Zhou Weiyi Huang Wei Hu Xinyu Feng Basic Medical College Guangxi Traditional Chinese Medical UniversityNanning 530005GuangxiChina College of Life Sciences Inner Mongolia UniversityHohhot 010070China College of Animal Science and Technology Guangxi UniversityNanning 530005GuangxiChina National Institute of Parasitic diseases Chinese Center for Disease Control and PreventionKey Laboratory of Parasite and Vector Biology of China Ministry of HealthWHO Collaborating Centre for Tropical DiseasesJoint Research Laboratory of Genetics and Ecology On Parasite-Host InteractionChinese Center for Disease Control and PreventionFudan University200025 ShanghaiChina Department of infectious diseases Huashan HospitalState Key Laboratory of Genetic EngineeringMinistry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringMinistry of Education Key Laboratory of Contemporary AnthropologySchool of Life SciencesFudan UniversityShanghai 200438China School of Global Health Chinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai 20025China One Health Center Shanghai Jiao Tong University-The University of EdinburghShanghai 20025China

Background:Food-borne parasitic diseases decrease food safety and threaten public *** snail species is an intermediate host for numerous human parasitic *** ollula has been reported as intermediate hosts of many zoonotic ***,we investigated the prevalence of zoonotic trematodes *** in Guangxi,China,and assessed their zoonotic ***:Snails were collected from 54 sites in 9 cities throughout *** snail and trematode larvae species were determined by combining morphological characteristics and molecular *** trematodes prevalence and constituent ratio were calculated and compared among different habitat *** trees of the trematode species were constructed using the neighbor-joining method with nuclear internal transcribed spacer 2(ITS2)*** developmental cycles of the isolated trematodes were examined by experimental infection in *** developmental characteristics ofEchinostoma revolutum was recorded by dissecting infected ducklings from 1-day post infection(dpi)to 10 ***:The overall prevalence of trematode larvae was 22.1%(1818/8238)*** from 11 sample *** together with molecular identification,showed ***,Australapatemon sp.,Hypoderaeum conoideum,Pharyngostomum cordatum,andEchinostoma ***,with the highest infection rate ***(13.0%).However,noFasciola larvae were *** trematodes prevalence and constituent ratio varied in two sub-biotypes(P<0.01).A neighbor-joining tree analysis of ITS2 sequences resulted in distinct monophyletic clades supported by sequences from isolated larvae with high bootstrap *** exposed *** infected withEchinostoma sp.,***,*** larvae were successfully *** animal model forEchinostoma revolutum was successfully *** matured from larvae to adult at 10 dpi in the intestine of the duck,and the devel

关键词： Orientogalba ollula Zoonotic trematode Intermediate host Prevalence ITS2

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Unmanned aerial vehicles:potential tools for use in zoonosis control

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infectious diseases of Poverty 2018年第1期7卷 480-485页

作者： Qing Yu Hui Liu Ning Xiao National Institute of Parasitic diseases Chinese Center for Disease Control and PreventionChinese Center for Tropical Diseases ResearchWHO Collaborating Centre for Tropical DiseasesNational Center for International Research on Tropical DiseasesMinistry of Science and TechnologyKey Laboratory of Parasite and Vector BiologyNational Health Comission of China207 Ruijin Er RoadShanghai 200025China Jinan Center for disease control and Prevention Jinan 250021ShandongChina

Unmanned aerial vehicles(UAVs)have become useful tools to extend human abilities and *** UAVs are being used for the surveillance of environmental factors related to the transmission of infectious *** have also been used for delivering therapeutic drugs and life-saving supplies to patients or isolated persons in extreme *** have been very few applications of UAVs for disease surveillance,control and prevention to ***,we foresee many uses for these machines in the fight against zoonotic *** control of zoonoses has been a big challenge as these diseases are naturally maintained in animal *** 868 reported zoonoses,echinococcosis(hydatid disease)is one of the most severe public health problems and listed as one of 17 neglected tropical diseases targeted for control by the World Health *** dogs(domestic or stray)play the most important role as definitive hosts in maintaining the transmission of ***,the actual contribution of wild canines to transmission has received little attention as yet,but should certainly not be *** paper summarizes the history of development and application of UAVs,with an emphasis on their potential use for zoonosis *** an example,we outline a pilot trial of echinococcosis control in the Qinghai-Tibet Plateau region,in which UAVs were used to deliver baits with praziquantel for wildlife *** data suggested that this is a cost-effective and efficient approach to the control of zoonotic diseases transmitted among wild animal populations.

关键词： control Echinococcosis Public health Unmanned aerial vehicles Wild animal Zoonosis

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Visceral Leishmaniasis--China,2015−2019

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China CDC weekly 2020年第33期2卷 625-628页

作者： Zhengbin Zhou Shan Lyu Yi Zhang Yuanyuan Li Shizhu Li Xiao-nong Zhou National Institute of Parasitic diseases Chinese Center for Disease Control and Prevention/Chinese Center for Tropical Diseases Research/Key Laboratory of Parasite and Vector BiologyMinistry of Health/WHO Collaborating Centre for Tropical Diseases/National Center for International Research on Tropical DiseasesMinistry of Science and TechnologyShanghaiChina

What is already known about this topic?Visceral leishmaniasis(VL)is an important vectorborne disease in rural areas of western *** spreading of VL made its prevention and control become more *** is added by this report?The number of VL cases decreased from 2015(n=498)to 2019(n=166).However,the mountain-type zoonotic visceral leishmaniasis(MT-ZVL)cases increased from 2015(n=82,16.5%)to 2019(n=122,73.5%).In addition,both number and proportion of imported cases increased from 2015(n=18,3.6%)to 2019(n=41,24.7%).The re-emergence of MT-ZVL was considerable;13 historically-endemic counties reported 48 indigenous *** and young children were the high risk population of VL(848,62.4%)followed by farmers(303,22.3%).What are the implications for public health practice?Both MT-ZVL and imported cases showed an increasing trend in ***,two actions are needed to control VL:1)to prevent re-emergence and spreading of MT-ZVL;and 2)to ensure timely diagnosis and appropriate treatment to avoid fatal VL cases,especially in non-endemic areas.

关键词： prevention diagnosis imported

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Public health implications of Yersinia enterocolitica investigation:an ecological modeling and molecular epidemiology study

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infectious diseases of Poverty 2023年第2期12卷 134-135页

作者： Yuan Yue Jinxin Zheng Mei Sheng Xiang Liu Qiong Hao Shunxian Zhang Shuai Xu Zhiguo Liu Xuexin Hou Huaiqi Jing Yang Liu Xuezhang Zhou Zhenjun Li Key Laboratory of the Ministry of Education for the Conservation and Utilization of Special Biological Resources of Western China Ningxia University Yinchuan People’s Republic of China State Key Laboratory for infectious disease Prevention and control National Institute for Communicable Disease Control and Prevention Chinese Center for Disease Control and Prevention Beijing People’s Republic of China Ningxia Hui Autonomous Region Food Testing and Research Institute Yinchuan People’s Republic of China Department of Nephrology Ruijin Hospital Institute of Nephrology Shanghai Jiao Tong University School of Medicine Shanghai People’s Republic of China School of Global Health Chinese Center for Tropical Diseases Research-Shanghai Jiao Tong University School of Medicine Shanghai People’s Republic of China Ningxia Hui Autonomous Region centre for disease control and Prevention Yinchuan People’s Republic of China Longhua Hospital Shanghai University of Traditional Chinese Medicine Shanghai People’s Republic of China Department of Computer Science Hong Kong Baptist University Hong Kong People’s Republic of China

Background Yersinia enterocolitica has been sporadically recovered from animals,foods,and human clinical samples in various regions of Ningxia,***,the ecological and molecular characteristics of ***,as well as public health concerns about infection in the Ningxia Hui Autonomous Region,remain *** study aims to analyze the ecological and molecular epidemiological characteristics of *** in order to inform the public health intervention strategies for the contains of related *** A total of 270 samples were collected for isolation[animals(n=208),food(n=49),and patients(n=13)],then suspect colonies were isolated and identified by the API20E biochemical identification system,serological tests,biotyping tests,and 16S ***,we used an ecological epidemiological approach combined with machine learning algorithms(general linear model,random forest model,and eXtreme Gradient Boosting)to explore the associations between ecological factors and the pathogenicity of ***,average nucleotide identity(ANI)estimation,single nucleotide polymorphism(SNP),and core gene multilocus sequence typing(cgMLST)were applied to characterize the molecular profile of isolates based on whole genome *** statistical test used single-factor analysis,Chi-square tests,t-tests/ANOVA-tests,Wilcoxon rank-sum tests,and Kruskal–Wallis *** A total of 270 isolates of Yersinia were identified from poultry and livestock(n=191),food(n=49),diarrhoea patients(n=13),rats(n=15),and hamsters(n=2).The detection rates of samples from different hosts were statistically different(χ^(2)=22.636,P<0.001).According to the relatedness clustering results,270 isolates were divided into 12 species,and ***(n=187)is a predominated *** isolates made up 52.4%(98/187),while non-pathogenic isolates made up 47.6%(89/187).Temperature and precipitation were strongly associated with the pathogenicity of the

关键词： Yersinia enterocolitica Ecological Machine learning Molecular epidemiology Core genome multilocus sequence typing Ningxia,China

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