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Chromosome-level genome assembly of Oncomelania hupensis: the intermediate snail host of Schistosoma japonicum

Infectious Diseases of Poverty 2024年第1期13卷 16-26页

作者： Qin Liu Lei Duan Yun-Hai Guo Li-Min Yang Yi Zhang Shi-Zhu Li Shan Lv Wei Hu Nan-Sheng Chen Xiao-Nong Zhou national Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention(Chinese Centerfor Tropical Diseases research) NHC Key Laboratory of Parasite and Vector BiologyWHO Collaborating Centre for Tropical DiseasesNational Center for International Research on Tropical DiseasesNational Key Laboratory of Intelligent Tracking and Forecasting for Infectious DiseasesShanghai 200025People's Republic of China School of Global Health Chinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai 200025People's Republic of China School of Life Science Fudan UniversityShanghai 200438People's Republic of China CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of OceanologyChinese Academy of SciencesQingdaoShandong 266071People'sRepublicofChina

Background Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and *** hupensis (Gastropoda: Pomatiopsidae) is the unique intermediate host ofS. japonicum. A complete genome sequence ofO. hupensis will enable the fundamental understanding of snail biology as well as its co-evolution with theS. japonicum parasite. Assembling a high-quality reference genome ofO. hupehensis will provide data for further research on the snail biology and controlling the spread ofS. *** The draft genome was de novo assembly using the long-read sequencing technology (PacBio Sequel II) and corrected with Illumina sequencing data. Then, using Hi-C sequencing data, the genome was assembled at the chromosomal level. CAFE was used to do analysis of contraction and expansion of the gene family and CodeML module in PAML was used for positive selection analysis in protein coding *** A total length of 1.46 Gb high-qualityO. hupensis genome with 17 unique full-length chromosomes (2n = 34) of the individual including a contig N50 of 1.35 Mb and a scaffold N50 of 75.08 Mb. Additionally, 95.03% of these contig sequences were anchored in 17 chromosomes. After scanning the assembled genome, a total of 30,604 protein-coding genes were predicted. Among them, 86.67% were functionally annotated. Further phylogenetic analysis revealed thatO. hupensis was separated from a common ancestor ofPomacea canaliculata andBellamya purificata approximately 170 million years ago. Comparing the genome ofO. hupensis with its most recent common ancestor, it showed 266 significantly expanded and 58 significantly contracted gene families (P < 0.05). Functional enrichment of the expanded gene families indicated that they were mainly involved with intracellular, DNA-mediated transposition, DNA integration and transposase *** Integrated use of multiple sequencing technol

关键词： Schistosomiasis Schistosoma japonicum Oncomelania hupensis Chromosome-level genome

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Evaluation of Real-Time PCR and Culturing for the Detection of Leptospires in Canine Samples

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Advances in Microbiology 2012年第2期2卷 162-170页

作者： Ahmed Ahmed Henricus L. B. M. Klaasen Mark van der Veen Hans van der Linden Marga G. A. Goris Rudy A. Hartskeerl MSD Animal Health Department Microbiological Research and Development Boxmeer The Netherlands who/fao/oie and national collaborating centre for reference and research on leptospirosis Department of Biomedical Research Royal Tropical Institute Amsterdam The Netherlands who/fao/oie and national collaborating centre for reference and research on leptospirosis Department of Biomedical Research Royal Tropical Institute Amsterdam The Netherlands

Validated real-time PCRs detecting leptospires for veterinary purposes are not readily available. This paper describes the prospective evaluation of a SYBR Green-based real-time PCR on serum samples collected from experimentally infected dogs. Compared to culturing, the assay had a diagnostic sensitivity and specificity of 91.7% and 90.0%, respectively. Culturing for part is complementary to PCR and preferably both should be applied for diagnosis and vaccine challenge experiments. In a subsequent prospective study on the dynamics of experimental infections with serovars Canicola and Copenhageni and serovar complex Bananal-Liangguang in young and adult dogs, the PCR was applied on serum samples in conjunction with culturing on blood, urine and kidney samples with the following results: 1) Leptospires persisted longer in the blood of young dogs than of adult ones;2) Numbers of viable leptospires in the blood are rapidly reduced but DNA remains occasionally detectable up to 7 days post infection;3) Appearance of viable leptospires in the urine follows a biphasic dynamics;4) EDTA hampers effective culturing from blood samples;5) Serovar Canicola persists longer in the blood of dogs than Copenhageni and Bananal-Liangguang. Together with a markedly higher recovery rate from kidney samples (71% compared to respectively 33% and 0% in young dogs), this probably reflects the adaptation power of Canicola to its canine maintenance host. Appearance of leptospires in the urine samples indicates that experimental infections have been successful. PCR presents a valuable adjunct to the diagnosis of veterinary leptospirosis and the follow-up in vaccine protection experiments.

关键词： leptospirosis Diagnosis PCR Evaluation Canine Experimental Infection Challenge Infection Kinetics

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Epidemiological and Virological Surveillance of Seasonal Influenza Viruses—China,2020–2021

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China CDC weekly 2021年第44期3卷 918-922页

作者： Weijuan Huang Xiyan Li Minju Tan Yanhui Cheng Tao Chen Hejiang Wei Xiaoxu Zeng Yiran Xie Jia Liu Ning Xiao Lei Yang Dayan Wang national Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and PreventionWHO Collaborating Centre for Reference and Research on InfluenzaKey Laboratory for Medical VirologyNational Health CommissionBeijingChina

Introduction:During the coronavirus disease 2019(COVID-19)pandemic,the circulation of seasonal influenza virus declined globally and remained below previous seasonal *** analyzed the results of the epidemiology,antigenic,and genetic characteristics,and antiviral susceptibilities of seasonal influenza viruses isolated from the mainland of China during October 5,2020 through September 5,2021,to better assess the risk of influenza during subsequent influenza season in 2021–***:Positive rates of influenza virus detection during this period were based on real-time polymerase chain reaction(PCR)detection by the Chinese national Influenza Surveillance Network laboratories,and isolated viruses from influenza positive samples were submitted to the Chinese national Influenza *** analyses for influenza viruses were conducted using the hemagglutination inhibition ***-generation sequencing was used for genetic *** were tested for resistance to antiviral medications using a phenotypic assay and next-generation ***:In southern China,the influenza positivity rate was elevated especially after March 2021 and was higher than the same period the previous year with the COVID-19 *** northern China,influenza positive rate peaked at Week 18 in 2021 and has declined since *** all isolated viruses were B/Victoria lineage viruses during the study period,and 37.3%of these viruses are antigenically similar to the reference viruses representing the vaccine components for the 2020–2021 and 2021–2022 Northern Hemisphere influenza *** seasonal influenza viruses were susceptible to neuraminidase inhibitors and endonuclease ***:Influenza activity has gradually increased in the mainland of China in 2021,although the intensity of activity is still lower than before the COVID-19 *** diversity of circulating influenza types/subtypes decreased,with the vast majority being B/Victoria lineage v

关键词： mainland season prevention

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SARS-CoV-2 Surveillance Through China Influenza Surveillance Information System—China,December 1,2022 to February 12,2023

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China CDC weekly 2023年第7期5卷 152-158页

作者： Xiaoxu Zeng Yiran Xie Xiaokun Yang Zhibin Peng Jing Tang Lei Yang Shuxia Lin Jun Han Yanping Zhang Dayan Wang national Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention/WHO Collaborating Centre for Reference and Research on InfluenzaBeijing MunicipalityChina Chinese Center for Disease Control and Prevention Beijing MunicipalityChina Key Laboratory for Medical Virology National Health CommissionBeijing MunicipalityChina

Introduction:The World Health Organization(who)proposed using influenza surveillance systems to carry out coronavirus disease 2019(COVID-19)surveillance due to the similarity between the two diseases in some respiratory *** assess the prevalence of COVID-19,we analyzed the influenzalike illness(ILI)and positive rate of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)detections in ILI patients reported to the influenza Surveillance Information System(CNISIS)since late ***:Data related to ILI were reported by national surveillance sentinel *** testing for SARS-CoV-2 and influenza viruses was conducted using real-time reverse transcription polymerase chain reaction(rRT-PCR)detection by the national influenza surveillance network *** data were reported to ***:Beginning on December 12,2022(Week 50),the ILI percentage increased dramatically,peaking in Week 51 at 12.1%.Subsequently,the ILI percentage began to decline rapidly from Week 52,2022,and by Week 6,2023(February 6-12),the ILI and ILI percentage had returned to the levels observed at the beginning of December *** December 1,2022 to February 12,2023,115,844 specimens were tested for both SARS-CoV-2 and influenza *** these,30,381(26.2%)were positive for SARSCoV-2 and 1,763(1.5%)were positive for influenza *** positive rate of SARS-CoV-2 tests peaked at 74.1%around December 23 and ***:Sentinel-based surveillance,previously established for influenza,is an effective way to track the circulation trend of SARS-CoV-2 during community-level *** was no coprevalence of SARS-CoV-2 and influenza virus during the outbreak of SARS-CoV-2,even during the winter influenza ***,it is important to remain vigilant for the potential rise of influenza activities following the COVID-19 epidemic.

关键词： winter December surveillance

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The year 2020,a milestone in breaking the vicious cycle of poverty and illness in China

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Infectious Diseases of Poverty 2020年第1期9卷 1-8页

作者： Yun-Ping Wang Xiao-Nong Zhou China national Health Development research centre National Health Commission of ChinaWHO Collaborating Centre for Health Systems StrengtheningBeijing 100044China national Institute of Parasitic Diseases at Chinese Center for Diseases Control and Prevention Chinese Center for Tropical Diseases ResearchShanghai 200025China who collaborating centre for Tropical Diseases National Center for International Research on Tropical DiseasesMinistry of Science and TechnologyKey Laboratory of Parasite and Vector BiologyMinistry of HealthShanghai 200025China School of Global Health Chinese Center for Tropical Diseases ResearchJiatong University School of MedicineShanghai 200025China

Marking the end of the five-year programme initiated by the Chinese Government to lift more than 70 million people out of poverty,the year 2020 is a *** alleviation has moved strongly forward in China and the major health indicators are now better than the average of all middle-and high-income ***,the dual burden of infectious and chronic diseases remains a challenge with respect to achieving the health target in the United Nations 2030 Agenda for sustainable development goals(SDGs).In 2015,about 44%of the poor population in China were impoverished by illness but already in 2018,multi-sectoral actions delivered by the Health-related Poverty Alleviation programme had reduced the number almost by *** the past three years 15 million poor people(98%of the poor population)with infectious and chronic diseases had been treated and taken care of thanks to financial support through multiple health insurance schemes and other governmental *** article discusses the lessons learnt with regard to health-related poverty alleviation in China with special reference to those still remaining impoverished by *** of the achievements reached and provision of basic needs to those still disadvantaged and in poor health will require a major improvement of accessibility to,and affordability of,health *** next step towards enhanced productivity and better living conditions will involve upgrading of the capacity of health professionals in the poor regions,promotion of coherent efforts in health-related poverty alleviation and rural revitalization *** an additional measure,data monitoring and research on health poverty alleviation should be strengthened as they are essential to generate the evidence and knowledge needed to support the move in the direction envisioned by the SDGs,and the new Healthy China 2030 programme.

关键词： Poverty alleviation Infectious diseases Poor population Health insurance Endemic diseases China Healthy China

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Achievements of the national malaria control and elimination program in the People’s Republic of China:the Atlas of Malaria Transmission in China

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Frontiers of Medicine 2023年第1期17卷 85-92页

作者： Jun Feng Li Zhang Zhigui Xia Shuisen Zhou Ning Xiao Xiao-Nong Zhou national Institute of Parasitic Diseases 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 DiseasesNational Center for International Research on Tropical DiseasesShanghai 200025China School of Global Health Chinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai 200025China

In 2017,China achieved the target of zero indigenous malaria case for the first time,and has been certified as malaria free by World Health Organization in *** further summarize the historical achievements and technical experiences of the elimination program,a project on the Roadmap Analysis and Verification for Malaria Elimination in China was carried *** of the project were compiled and published as the Atlas of Malaria Transmission in China(The Atlas).The Atlas using modern digital information technologies,has been supported by various data from 24 malaria endemic provinces of China since 1950,to assess the changes in malaria epidemic patterns from 1950 to 2019 at national and provincial *** Atlas is designed as two volumes,including a total of 1850 thematic maps and more than 130 charts,consisting of introductory maps,thematic maps of malaria epidemic and control at national and provincial *** objectively and directly shows the epidemic history,evolution process,and great achievements of the national malaria control and elimination program in *** Atlas has important reference value for summing up historical experience in the national malaria elimination program of China,and malaria control and elimination in other endemic countries in the world.

关键词： malaria transmission control elimination China atlas

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Recognizing and monitoring infectious sources of schistosomiasis by developing deep learning models with high-resolution remote sensing images

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Infectious Diseases of Poverty 2023年第1期12卷 24-35页

作者： Jing-Bo Xue Shang Xia Xin-Yi Wang Lu-Lu Huang Liang-Yu Huang Yu-Wan Hao Li-Juan Zhang Shi-Zhu Li national Institute of Parasitic Diseases 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 DiseasesNational Center for International Research On Tropical DiseasesShanghai 200025China School of Global Health Chinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai 200025China

Background China is progressing towards the goal of schistosomiasis elimination,but there are still some problems,such as difficult management of infection source and snail *** study aimed to develop deep learning models with high-resolution remote sensing images for recognizing and monitoring livestock bovine,which is an intermediate source of Schistosoma japonicum infection,and to evaluate the effectiveness of the models for real-world *** The dataset of livestock bovine’s spatial distribution was collected from the Chinese national Platform for Common Geospatial Information *** high-resolution remote sensing images were further divided into training data,test data,and validation data for model *** recognition models based on deep learning methods(ENVINet5 and Mask R-CNN)were developed with reference to the training *** performance of the developed models was evaluated by the performance metrics of precision,recall,and *** A total of 50 typical image areas were selected,1125 bovine objectives were labeled by the ENVINet5 model and 1277 bovine objectives were labeled by the Mask R-CNN *** the ENVINet5 model,a total of 1598 records of bovine distribution were *** model precision and recall were 81.9%and 80.2%,*** F1 score was *** the Mask R-CNN mode,1679 records of bovine objectives were *** model precision and recall were 87.3%and 85.2%,*** F1 score was *** applying the developed models to real-world schistosomiasis-endemic regions,there were 63 bovine objectives in the original image,53 records were extracted using the ENVINet5 model,and 57 records were extracted using the Mask R-CNN *** successful recognition ratios were 84.1%and 90.5%for the respectively developed *** The ENVINet5 model is very feasible when the bovine distribution is low in structure with few *** Mask R-CNN model has a good framework de

关键词： Deep learning High-resolution remote sensing Recognizing Monitoring Infectious source Schistosomiasis

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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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Evaluation of intrahepatic manifestation and distant extrahepatic disease in alveolar echinococcosis

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World Journal of Gastroenterology 2020年第29期26卷 4302-4315页

作者： Tilmann Graeter Hai-Hua Bao Rong Shi Wen-Ya Liu Wei-Xia Li Yi Jiang Julian Schmidberger Eleonore Brumpt Eric Delabrousse Wolfgang Kratzer Department of Diagnostic and Interventional Radiology University Hospital UlmUlm 89081Germany Qinghai University Qinghai University First Affiliated HospitalXining 810001Qinghai ProvinceChina University First Affiliated HospitalWHO Collaborating Centre on Prevention and Care Management of EchinococcosisUrumqi 830054Xinjiang Uyghur Autonomous RegionChina Department of Internal Medicine I University Hospital UlmUlm 89081Germany who collaborating centre on Prevention and Treatment of Human Echinococcosis/national French reference centre for Echinococcosis University Bourgogne Franche-Comtéand Besançon University HospitalBesançon 25030France

BACKGROUND The main endemic areas of alveolar echinococcosis(AE)are in Central Europe and Western *** the infiltration of intrahepatic vascular and bile duct structures as well as extrahepatic disease can lead to further complications and may increase morbidity in patients with *** To evaluate vascular/biliary involvement in hepatic AE and its distant extrahepatic disease manifestations in an international collective was the *** Consecutively,five experienced examiners evaluated contrast-enhanced abdominal computed tomography(CT)scans for 200 patients with hepatic AE of each of four locations(n=50)in Germany,France and ***,we retrospectively included the 50 most recent abdominal contrast-enhanced CT examinations at each center,performed because of hepatic AE from September 21,2007 to March 21,*** liver lesions were classified according to the echinococcosis multilocularis Ulm classification for CT(EMUC-CT).Distant extrahepatic manifestations were documented either by whole body positron emission tomography–CT or with the addition of thoracic CT and cranial magnetic resonance ***/biliary involvement of the hepatic disease as well as the presence of distant extrahepatic manifestations were correlated with the EMUC-CT types of liver *** analysis was performed using SAS Version 9.4(SAS Institute Inc.,Cary,NC,United States).RESULTS Distant extrahepatic AE manifestations were significantly more frequent in China than in Europe(P=0.0091).A significant relationship was found between the presence of distant extrahepatic disease and AE liver lesion size(P=0.0075).Vascular/biliary structures were involved by the liver lesions significantly more frequently in China than in Europe(P<0.0001),and vascular/biliary involvement depended on lesion *** morphological types of AE liver lesions led to varying frequencies of vascular/biliary involvement and were associated with different frequencies of distant extrahe

关键词： Alveolar echinococcosis Echinococcus multilocularis Echinococcus multilocularis Ulm classification for computed tomography Vascular/biliary involvement Extrahepatic manifestation XUUB project

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Epidemiological and virological surveillance of influenza viruses in China during 2020–2021

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Infectious Diseases of Poverty 2022年第3期11卷 101-101页

作者： Wei-juan Huang Yan-hui Cheng Min-ju Tan Jia Liu Xi-yan Li Xiao-xu Zeng Jing Tang He-jiang Wei Tao Chen Lei Yang Yi-ran Xie Jia-ying Yang Ning Xiao Da-yan Wang national Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and PreventionWHO Collaborating Centre for Reference and Research on InfluenzaKey Laboratory for Medical Virology and Viral DiseasesNational Health CommissionBeijingChina

Background: During the coronavirus disease 2019(COVID-19)pandemic,seasonal influenza activity declined globally and remained below previous seasonal levels,but intensified in China since *** measures to COVID-19 accompanied by different epidemic characteristics of influenza in different regions of the *** better respond to influenza outbreaks under the COVID-19 pandemic,we analyzed the epidemiology,antigenic and genetic characteristics,and antiviral susceptibility of influenza viruses in the mainland of China during 2020–***: Respiratory specimens from influenza like illness cases were collected by sentinel hospitals and sent to network laboratories in Chinese national Influenza Surveillance *** mutation analysis of influenza virus isolates was performed by hemagglutination inhibition ***-generation sequencing was used for genetic *** also conducted molecular characterization and phylogenetic analysis of circulating influenza *** were tested for resistance to antiviral medications using phenotypic and/or sequence-based ***: In the mainland of China,influenza activity recovered in 2021 compared with that in 2020 and intensified during the traditional influenza winter season,but it did not exceed the peak in previous *** all viruses isolated during the study period were of the B/Victoria lineage and were characterized by genetic diversity,with the subgroup 1A.3a.2 viruses currently predominated.37.8%viruses tested were antigenically similar to reference viruses representing the components of the vaccine for the 2020–2021 and 2021–2022 Northern Hemisphere influenza *** addition,China has a unique subgroup of 1A.3a.1 *** viruses tested were sensitive to neuraminidase inhibitors and endonuclease inhibitors,except two B/Victoria lineage viruses identified to have reduced sensitivity to neuraminidase ***: Influenza activity increased in the mainland of

关键词： Influenza B/Victoria lineage viruses Epidemiological Virological Surveillance

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