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Prediction of H7N9 epidemic in China

Chinese Medical Journal 2014年第2期127卷 254-260页

作者： Zhang Zhaojie Xia Yao Lu Yi Yang Jingchao Zhang Luwen Su Hui Lin Lili Wang Guoling Wang Tongmei Lin Shao Guo Zhongmin Lu Jiahai School of Public Health Sun Yat-sen University GuangzhouGuangdong 510030 China Department of Earth Science Sun Yat-sen University Guangzhou Guangdong 510275 China School of Public Health Southern Medical University Guangzhou Guangdong 510515 China Key Laboratory of Tropical Disease Control Ministry of Education Guangzhou Guangdong 510080 China Haizhu District Center for Disease Control and Prevention Guangzhou Guangdong 510288 China Department of Atmospheric Science School of Environmental Science and Engineering Sun Yat-sen University Guangzhou Guangdong 510275 China School of Public Health University at Albany State University of New York Rensselaer New York USA

Background In March 2013,human cases of infection with a novel A （H7N9） influenza virus emerged in China.The epidemic spread quickly and as of 6 May 2013,there were 129 confirmed cases.The purpose of this study was to analyze the epidemiology of the confirmed cases,determine the impacts of bird migration and temperature changes on the H7N9 epidemic,predict the future trends of the epidemic,explore the response patterns of the government and propose preventive suggestions.Methods The geographic,temporal and population distribution of all cases reported up to 6 May 2013 were described from available records.Risk assessment standard was established by analysing the temperature and relative humidity records during the period of extensive outbreak in three epidemic regions in eastern China,including Shanghai,Zhejiang and Jiangsu provinces.Risk assessment maps were created by combining the bird migration routes in eastern China with the monthly average temperatures from May 1993 to December 2012 nationwide.Results Among the confirmed cases,there were more men than women,and 50.4％ were elderly adults （age ＞61 years）.The major demographic groups were retirees and farmers.The temperature on the days of disease onset was concentrated in the range of 9℃-19℃; we defined 9℃-19℃ as the high-risk temperature range,0℃-9℃ or 19℃-25℃ as medium risk and ＜0℃ or ＞25℃ as low risk.The relative humidity on the days of disease onset ranged widely from 25％ to 99％,but did not correlate with the incidence of infection.Based on the temperature analysis and the eastern bird migration routes,we predicted that after May,the high-risk region would move to the northeast and inland,while after September,it would move back to north China.Conclusions Temperature and bird migration strongly influence the spread of the H7N9 virus.In order to control the H7N9 epidemic effectively,Chinese authorities should strengthen the surveillance of migrating birds,increase poultry and environmental sampling,improve live poultry selling and husbandry patterns and m

关键词： H7N9 prediction bird migration passive response pattern

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A grid-based clustering algorithm for wild bird distribution

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Frontiers of Computer Science 2013年第4期7卷 475-485页

作者： Yuwei WANG Yuanchun ZHOU Ying LIU Ze LUO Danhuai GUO Jing SHAO Fei TAN Liang WU Jianhui LI Baoping YAN Computer Network Information Center Chinese Academy of Sciences Beijing 100190 China University of Chinese Academy of Sciences Beijing 100049 China Research Center on Fictitious Economy and Data Science Chinese Academy of Sciences Beijing 100190 China

Advanced satellite tracking technologies provide biologists with long-term location sequence data to understand movement of wild birds then to find explicit correlation between dynamics of migratory birds and the spread of avian influenza. In this paper, we propose a hierarchical clustering algorithm based on a recursive grid partition and kernel density estimation （KDE） to hierarchically identify wild bird habitats with different densities. We hierarchically cluster the GPS data by taking into account the following observations： 1） the habitat variation on a variety of geospatial scales; 2） the spatial variation of the activity patterns of birds in different stages of the migration cycle. In addition, we measure the site fidelity of wild birds based on clustering. To assess effectiveness, we have evaluated our system using a large-scale GPS dataset collected from 59 birds over three years. As a result, our approach can identify the hierarchical habitats and distribution of wild birds more efficiently than several commonly used algorithms such as DBSCAN and DENCLUE.

关键词： hierarchical clustering bird migration kerneldensity estimation grid partition

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Weather conditions affect spring and autumn migration of Siberian leaf warblers

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Avian Research 2018年第4期9卷 321-328页

作者： Lászlo Bozo Tibor Csorgo Wieland Heim Department of Systematic Zoology and Ecology Eotvos Loránd UniversityPázmány Péter sétány 1/CBudapest 1117Hungary Department of Anatomy Cell-and Developmental BiologyEotvos Loránd UniversityPázmány Péter sétány 1/CBudapest 1117Hungary Institute of Landscape Ecology University of MünsterHeisenbergstraBe 248149 MünsterGermany

Background: Weather effects on bird migration are well-studied among Passerines moving from Europe to Africa or within the American flyway systems. However, little is known about the weather impact on songbirds migrating along the East Asian flyway. Our study aims to describe the effects of various weather elements on the migration of four species of leaf warblers by using bird ringing data from a stopover site in Far East Russia.Methods: We determined the migration periods for each species and included maximum temperature, precipitation, air pressure, wind speed and wind direction in general linearized mixed models to predict the number of migrating birds.Results: We found strong impacts of weather variables on the number of trapped warblers during spring and autumn migration. Preferred or avoided weather conditions were similar among the studied species. All species seem to migrate preferably during warm, calm days without precipitation. A positive effect of tail winds was only confirmed in autumn, but in spring, most birds were trapped during crosswinds(eastern or western winds).Conclusion: The studied species might exhibit a loop migration, leading to a more longitudinal(from east to west) migration pattern in our study area during spring. Relationships between weather variables and the number of migrating individuals were much stronger during autumn. We argue that birds during spring migration would continue migration under sub-optimal conditions, as a result of strong competition to arrive earliest on their breeding grounds.

关键词： Phylloscopus bird migration Weather East Asian flyway

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Modeling Lyme disease transmission

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Infectious Disease Modelling 2017年第2期2卷 229-243页

作者： Yijun Lou Jianhong Wu Department of Applied Mathematics The Hong Kong Polytechnic UniversityKowloonHong Kong Department of Mathematics and Statistics York UniversityTorontoOntarioM3J 1P3Canada

Lyme disease,a typical tick-borne disease,imposes increasing global public health challenges.A growing body of theoretical models have been proposed to better understand various factors determining the disease risk,which not only enrich our understanding on the ecological cycle of disease transmission but also promote new theoretical developments on model formulation,analysis and simulation.In this paper,we provide a review about the models and results we have obtained recently on modeling and analyzing Lyme disease transmission,with the purpose to highlight various aspects in the ecological cycle of disease transmission to be incorporated,including the growth of ticks with different stages in the life cycle,the seasonality,host diversity,spatial disease pattern due to host short distance movement and bird migration,co-infection with other tick-borne pathogens,and climate change impact.

关键词： Mathematical model Lyme disease Tick-borne disease Basic reproduction number Seasonality Spatial model Biodiversity Co-infection bird migration

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Identifying key bird species and geographical hotspots of avian influenza A(H7N9)virus in China

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Infectious Diseases of Poverty 2018年第1期7卷 1019-1029页

作者： Benyun Shi Xiao-Ming Zhan Jin-Xin Zheng Hongjun Qiu Dan Liang Yan-Ming Ye Guo-Jing Yang Yang Liu Jiming Liu School of Cyberspace Hangzhou Dianzi UniversityHangzhou 310018People’s Republic of China School of Computer Science and Technology Hangzhou Dianzi UniversityHangzhou 310018People’s Republic of China Jiangsu Institute of Parasitic Diseases Wuxi 214064People’s Republic of China Department of Epidemiology and Public Healthy Swiss Tropical and Public Health InstituteBaselSwitzerland University of Basel BaselSwitzerland State Key Laboratory of Biocontrol Department of Ecology and School of Life SciencesSun Yat-Sen UniversityGuangzhou 510275People’s Republic of China Department of Computer Science Hong Kong Baptist UniversityKowloon TongHong KongPeople’s Republic of China

Background:In China since the first human infection of avian influenza A(H7N9)virus was identified in 2013,it has caused serious public health concerns due to its wide spread and high mortality rate.Evidence shows that bird migration plays an essential role in global spread of avian influenza viruses.Accordingly,in this paper,we aim to identify key bird species and geographical hotspots that are relevant to the transmission of avian influenza A(H7N9)virus in China.Methods:We first conducted phylogenetic analysis on 626 viral sequences of avian influenza A(H7N9)virus isolated in chicken,which were collected from the Global Initiative on Sharing All Influenza Data(GISAID),to reveal geographical spread and molecular evolution of the virus in China.Then,we adopted the cross correlation function(CCF)to explore the relationship between the identified influenza A(H7N9)cases and the spatiotemporal distribution of migratory birds.Here,the spatiotemporal distribution of bird species was generated based on bird observation data collected from China bird Reports,which consists of 157272 observation records about 1145 bird species.Finally,we employed a kernel density estimator to identify geographical hotspots of bird habitat/stopover that are relevant to the influenza A(H7N9)infections.Results:Phylogenetic analysis reveals the evolutionary and geographical patterns of influenza A(H7N9)infections,where cases in the same or nearby municipality/provinces are clustered together with small evolutionary differences.Moreover,three epidemic waves in chicken along the East Asian-Australasian flyway in China are distinguished from the phylogenetic tree.The CCF analysis identifies possible migratory bird species that are relevant to the influenza A(H7N9)infections in Shanghai,Jiangsu,Zhejiang,Fujian,Jiangxi,and Guangdong in China,where the six municipality/provinces account for 91.2%of the total number of isolated H7N9 cases in chicken in GISAID.Based on the spatial distribution of identified bird species,geographical hotspots are furt

关键词： Avian influenza virus bird migration Geographical hotspots Phylogenetic analysis Cross correlation function

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Colour-ring wear and loss effects in citizen science mark-resighting studies

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Avian Research 2019年第2期10卷 148-162页

作者： Andrew M.Allen Bruno J.Ens Martijn van de Pol Henk van der Jeugd Magali Frauendorf Henk-Jan van der Kolk Kees Oosterbeek Jeroen Nienhuis Eelke Jongejans Department of Animal Ecology and Physiology Radboud University6500 GL NijmegenThe Netherlands Sovon Dutch Centre for Field Ornithology 6503 GANijmegen and Sovon-Texel1790 AB Den BurgThe Netherlands Department of Animal Ecology Netherlands Institute of Ecology NIOOKNAW6708 PB WageningenThe Netherlands Dutch Centre for Avian migration and Demography 6700 AB WageningenThe Netherlands Centre for Avian Population Studies WageningenThe Netherlands

Background: Ring wear and loss may have important consequences for mark-recapture studies that aim to estimate survival trends. Our study quantifies the rates of wear and loss from a long-running colour-ringing project of the Eurasian Oystercatcher (Haematopus ostralegus) in the Netherlands. Methods: Our analysis included 8909 colour-ringed oystercatchers with 118,071 resightings, predominantly ringed and observed by citizen scientists. We quantified how ring wear and loss may vary with ring colour and age, and how this may impact resighting probabilities. We then determined how ring loss may impact survival estimates and resighting probabilities of mark-recapture models by simulating four scenarios of how citizen scientists may resight and report birds with lost colour rings. Results: Annual rates of colour ring loss averaged 2.5% compared with 1% for ring wear, but lost rings also had a higher reporting probability (31.2%) than worn rings (10.3%). Lost rings may not directly impact survival estimates since 50% of oystercatchers with lost rings could still be uniquely identified. Ring wear and loss rapidly increased between 10 and 15 years after ringing. Rates of ring loss were comparable amongst ring colours, but the wear rate appeared higher for red and white rings compared to other colours. Rates of ring wear and loss varied significantly amongst different regions in our study, which were characterised as having different habitat features. Differential rates of ring wear may have important implications for studies conducted over large geographical scales or of multiple species. Conclusions: Based on simulations of ring loss in our population, estimates of apparent survival may be 0.3–1.2% lower whilst the impact of ring wear was deemed even lower. We developed a table of recommendations containing advice for ring fitting, data collection, study design, and mark-recapture analyses, so that future colour-ringing studies can benefit from our experiences in collecting and analysing data of ring wear and loss thro

关键词： Bias bird migration Citizen science Colour-ring Mark-recapture Shorebirds Survival

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