Epidemic characteristics, high-risk townships and space-time clusters of human brucellosis in Shanxi Province of China, 2005–2014

BACKGROUND: Brucellosis, one of the world's most important zoonosis, has been re-emerging in China. Shanxi Province, located in northern China, where husbandry development has been accelerated in recent years, has a rather high incidence of human brucellosis but drew little attention from the researchers. This study aimed to describe the changing epidemiology of human brucellosis in Shanxi Province from 2005 to 2014 and explore high-risk towns and space-time clusters for elucidating the necessity of decentralizing disease control resource to township level in epidemic regions, particularly in hotspot areas.METHODS: We extracted data from the Chinese National Notifiable Infectious Disease Reporting System to describe the incidence and spatiotemporal distribution of human brucellosis in Shanxi Province. Geographic information system was used to identify townships at high risk for the disease. Space-Time Scan Statistic was applied to detect the space-time clusters of human brucellosis during the past decade.RESULTS: From 2005 to 2014, a total of 50,002 cases of human brucellosis were recorded in Shanxi, with a male-to-female ratio of 3.9:1. The reported incidence rate increased dramatically from 7.0/100,000 in 2005 to 23.5/100,000 in 2014, with an average annual increase of 14.5%. There were still 33.8% cases delaying diagnosis in 2014. The proportion of the affected towns increased from 31.5% in 2005 to 82.5% in 2014. High-risk towns spread from the north to the center and then south of Shanxi Province, which were basins and adjacent highlands suitable for livestock cultivation. During the past decade, there were 55 space-time clusters of human brucellosis detected in high risk towns; the clusters could happen in any season. Some clusters' location maintained stable over time.CONCLUSIONS: During the last decade, Shanxi province's human brucellosis epidemic had been aggravated and high-risk areas concentrated in some towns located in basins and adjacent highlands. Space-time clusters existed and some located steadily over time. Quite a few cases still missed timely diagnosis. Greater resources should be allocated and decentralized to mitigate the momentum of rise and improve the accessibility of prompt diagnosis treatment in the high-risk townships

Genomic epidemiology of a densely sampled COVID-19 outbreak in China.

Analysis of genetic sequence data from the SARS-CoV-2 pandemic can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic epidemiological analysis has focused on geographically distributed data sets with few isolates in any given location. Here, we report an analysis of 20 whole SARS- CoV-2 genomes from a single relatively small and geographically constrained outbreak in Weifang, People's Republic of China. Using Bayesian model-based phylodynamic methods, we estimate a mean basic reproduction number (R 0) of 3.4 (95% highest posterior density interval: 2.1-5.2) in Weifang, and a mean effective reproduction number (Rt) that falls below 1 on 4 February. We further estimate the number of infections through time and compare these estimates to confirmed diagnoses by the Weifang Centers for Disease Control. We find that these estimates are consistent with reported cases and there is unlikely to be a large undiagnosed burden of infection over the period we studied

The Socioeconomic and Ecological Drivers of Avian Influenza Risks in China and at the International Level

abstract: Avian influenzas are zoonoses, or pathogens borne by wildlife and livestock that can also infect people. In recent decades, and especially since the emergence of highly pathogenic avian influenza (HPAI) H5N1 in 1996, these diseases have become a significant threat to animal and public health across the world. HPAI H5N1 has caused severe damage to poultry populations, killing, or prompting the culling of, millions of birds in Asia, Africa, and Europe. It has also infected hundreds of people, with a mortality rate of approximately 50%. This dissertation focuses on the ecological and socioeconomic drivers of avian influenza risk, particularly in China, the most populous country to be infected. Among the most significant ecological risk factors are landscapes that serve as “mixing zones” for wild waterfowl and poultry, such as rice paddy, and nearby lakes and wetlands that are important breeding and wintering habitats for wild birds. Poultry outbreaks often involve cross infections between wild and domesticated birds. At the international level, trade in live poultry can spread the disease, especially if the imports are from countries not party to trade agreements with well-developed biosecurity standards. However, these risks can be mitigated in a number of ways. Protected habitats, such as Ramsar wetlands, can segregate wild bird and poultry populations, thereby lowering the chance of interspecies transmission. The industrialization of poultry production, while not without ethical and public health problems, can also be risk-reducing by causing wild-domestic segregation and allowing for the more efficient application of surveillance, vaccination, and other biosecurity measures. Disease surveillance is effective at preventing the spread of avian influenza, including across international borders. Economic modernization in general, as reflected in rising per-capita GDP, appears to mitigate avian influenza risks at both the national and sub-national levels. Poultry vaccination has been effective in many cases, but is an incomplete solution because of the practical difficulties of sustained and widespread implementation. The other popular approach to avian influenza control is culling, which can be highly expensive and raise ethical concerns about large-scale animal slaughter. Therefore, it is more economically efficient, and may even be more ethical, to target the socio-ecological drivers of avian influenza risks, including by implementing the policies discussed here.Dissertation/ThesisDoctoral Dissertation Biology 201

Division of Public Health Systens abd Workforce Development 2009 annual report

In 2009, the U.S. Centers for Disease Control and Prevention (CDC) went through an agency-wide reorganization that led to a restructuring of our division and resulted in a name change. Our Divi- sion of Global Public Health Capacity Development was renamed Division of Public Health Systems and Workforce Development. This organizational restructuring more accurately reflects CDC\ue2\u20ac\u2122s new goal in the arena of global public health and allows us to better work with partners to strengthen capacity of countries around the world to improve their public health systems and build up their public health workforce.Throughout these organizational changes, we remain committed to spearhead efforts to improve global health through medical technology, international coalitions, government interventions, and basic behavior changes.Two of our long-standing programs are the Field Epidemiology Training Program (FETP) and the Field Epidemiology and Laboratory Training Program (FELTP), which are modeled after CDC\ue2\u20ac\u2122s Epi- demic Intelligence Service. Since 1980, these programs have been growing steadily and we have helped establish more than 30 FETPs or FELTPs that have produced more than 2,000 graduates. As of December 2009, we are supporting 12 FETPs or FELTPs, covering 23 countries, with the help of 14 resident advisors who provide direct program support on the ground. We are also in the process of establishing new programs in 7 regions, totaling 12 countries.Another major component of our work resides in helping countries develop or strengthen the management skills of their public health leaders through targeted country management capacity building programs. We are currently leading efforts in six countries. These programs are developed by our division\ue2\u20ac\u2122s Sustainable Management Development Program.Director\ue2\u20ac\u2122s letter -- Division overview -- Division-supported FETPs and FELTPs -- FELTPs in development -- Self-sustained FETPs and FELTPs -- Management capacity building programs -- Other division projects -- Appendices: Publications and presentations; Frequently used acronyms

Emerging infectious diseases

Emerging Infectious Diseases is providing access to these abstracts on behalf of the ICEID 2012 program committee (www.iceid.org), which performed peer review. Emerging Infectious Diseases has not edited or proofread these materials and is not responsible for inaccuracies or omissions. All information is subject to change. Comments and corrections should be brought to the attention of the authors.Influenza preparedness: lessons learned -- Policy implications and infectious diseases -- Improving preparedness for infectious diseases -- New or rapid diagnostics -- Foodborne and waterborne infections -- Effective and sustainable surveillance platforms -- Healthcare-associated infections -- Molecular epidemiology -- Antimicrobial resistance -- Tropical infections and parasitic diseases -- H1N1 influenza -- Risk Assessment -- Laboratory Support -- Zoonotic and Animal Diseases -- Viral Hepatitis -- E1. Zoonotic and animal diseases -- E2. Vaccine issues -- E3. H1N1 influenza -- E4. Novel surveillance systems -- E5. Antimicrobial resistance -- E6. Late-breakers I -- Antimicrobial resistance -- Influenza preparedness: lessons learned -- Zoonotic and animal diseases -- Improving preparedness for infectious diseases -- Laboratory support -- Early warning systems -- H1N1 influenza -- Policy implications and infectious diseases -- Modeling -- Molecular epidemiology -- Novel surveillance systems -- Tropical infections and parasitic diseases -- Strengthening public health systems -- Immigrant and refugee health -- Foodborne and waterborne infections -- Healthcare-associated infections -- Foodborne and waterborne infections -- New or rapid diagnostics -- Improving global health equity for infectious diseases -- Vulnerable populations -- Novel agents of public health importance -- Influenza preparedness: lessons learned -- Molecular epidemiology -- Zoonotic and animal diseases -- Vaccine-preventable diseases -- Outbreak investigation: lab and epi response -- H1N1 influenza -- laboratory support -- effective and sustainable surveillance platforms -- new vaccines -- vector-borne diseases and climate change -- travelers' health -- J1. Vectorborne diseases and climate change -- J2. Policy implications and infectious diseases -- J3. Influenza preparedness: lessons learned -- J4. Effective and sustainable surveillance platforms -- J5. Outbreak investigation: lab and epi response I -- J6. Late-breakers II -- Strengthening public health systems -- Bacterial/viral coinfections -- H1N1 influenza -- Novel agents of public health importance -- Foodborne and waterborne infections -- New challenges for old vaccines -- Vectorborne diseases and climate change -- Novel surveillance systems -- Geographic information systems (GIS) -- Improving global health equity for infectious diseases -- Vaccine preventable diseases -- Vulnerable populations -- Laboratory support -- Prevention challenges for respiratory diseases -- Zoonotic and animal diseases -- Outbreak investigation: lab and epi response -- Vectorborne diseases and climate change -- Outbreak investigation: lab and epi response -- Laboratory proficiency testing/quality assurance -- Effective and sustainable surveillance platforms -- Sexually transmitted diseases -- H1N1 influenza -- Surveillance of vaccine-preventable diseases -- Foodborne and waterborne infections -- Role of health communication -- Emerging opportunistic infections -- Host and microbial genetics -- Respiratory infections in special populations -- Zoonotic and animal diseases -- Laboratory support -- Antimicrobial resistance -- Vulnerable populations -- Global vaccine initiatives -- Tuberculosis -- Prevention challenges for respiratory diseases -- Infectious causes of chronic diseases -- O1. Outbreak investigation: lab and epi response II -- O2. Prevention challenges for respiratory diseases -- O3. Populations at high risk for infectious diseases -- O4. Foodborne and waterborne infections -- O5. Laboratory support: surveillance and monitoring infections -- O6. Late-breakers IIIAbstracts published in advance of the conference

Potential impact of climate change and water resources development on the epidemiology of schistosomiasis in China

Schistosomiasis japonica, caused by the blood fluke Schistosoma japonicum, has been endemic in China since ancient times. An estimated 11 million people were infected in the mid-1950s. Recognizing the huge public health significance and the economic impact of the disease, the central government of China implemented a large-scale control programme, which has been sustained and constantly adapted over the past half century. Today, the endemic areas are mainly confined to the lake and marshland regions along the Yangtze River in five provinces, namely Jiangsu, Anhui, Jiangxi, Hunan and Hubei. It is estimated that currently about 800,000 people are infected and that 40 million people are at risk of infection. Historically, the northern geographical limit where schistosomiasis transmission occurred was around the 33°15’ N latitude (e.g. in Baoying county, Jiangsu province), governed by low temperature thresholds. Based on various climate models, the Intergovernmental Panel of Climate Change (IPCC) recently concluded that the Earth has warmed by approximately 0.6°C over the past 100 years. This unusual warming has been particularly pronounced during the last three decades. There is growing consensus that the global trend of climate warming will continue in the 21st century. It has been suggested that climate change could impact on the distribution of the intermediate host snail of S. japonicum, i.e. Oncomelania hupensis. The frequency and transmission dynamics of schistosomiasis can also be affected by waterresource development and management. Among others, the South-to-North Water Transfer (SNWT) project” is currently under construction in China, which intends to divert water from South (the snail-infested Yangtze River) to North (Beijing and Tianjing) via the lakes of Gaoyou, Hongze and others. The implementation and operation of this project could further amplify the negative effects of climate change and facilitate the northward spread of O. hupensis. The main objective of this PhD thesis was to explore the potential impact of climate change and the SNWT project on the future distribution of schistosomiasis japonica, particularly in eastern China. The techniques used were geographic information system (GIS) and remote sensing (RS), coupled with Bayesian spatial statistics, which have become key tools for disease mapping and prediction. First, we reviewed the application of GIS/RS techniques for the epidemiology and control of schistosomiasis in China. The applications included mapping prevalence and intensity data of S. japonicum at a large scale, and identifying and predicting suitable habitats for O. hupensis at a small scale. Other prominent applications were the prediction of infection risk due to ecological transformations, particularly those induced by floods and water-resource development projects, and the potential impact of climate change. We discussed the limitations of the previous work, and outlined potential new applications of GIS/RS techniques, namely quantitative GIS, WebGIS and the utilization of emerging satellite-derived data, as they hold promise to further enhance infection risk mapping and disease prediction. We also stressed current research needs to overcome some of the remaining challenges of GIS/RS applications for schistosomiasis, so that further and sustained progress can be made towards the ultimate goal to eliminate the disease from China. Second, recognizing the advantages of combining GIS/RS techniques with advanced spatial statistical approaches, we developed Bayesian spatio-temporal models to analyze the relationship between key climatic factors and the risk of schistosomiasis infection. We used parasitological data collected annually from 1990 to 1998 by means of cross-sectional surveys carried out in 47 counties of Jiangsu province. Climatic factors, namely land surface temperature (LST) and normalized difference vegetation index (NDVI), were obtained from satellite sensors. Our analysis suggested a negative association between NDVI and the risk of S. japonicum infection, whereas an increase in LST contributed to a significant increase in S. japonicum infection prevalence. Third, in order to better understand the changes in the frequency and transmission dynamics of schistosomiasis in a warmer future China, a series of laboratory experiments were conducted to assess the effect of temperature on the parasite-intermediate host snail interaction. We found a positive linear relationship between the development of. S. japonicum larvae harboured in O. hupensis and temperature. In snails kept at 15.3°C, S. japonicum larvae tend to halt their development, while peak development occurs at 30°C. The temperature at which half of the snails were in hibernation is 6.4°C. A statistically significant positive association was observed between temperature and oxygen intake of O. hupensis at temperatures below 13.0°C. We also detected a logistic relationship between snails’ oxygen intake and their hibernation rate. Our results underscored the important role temperature plays both for the activity of O. hupensis and the development of S. japonicum larvae harboured in the intermediate host snail. Fourth, to substantiate the claim that global warming might alter the frequency and transmission dynamics of S. japonicum in China, we conducted a time-series analysis from 1972-2002, using temperature data from 39 counties of Jiangsu province. Using annual growing degree days (AGDDs) with a temperature threshold of 15.3°C, we forecasted changes in S. japonicum transmission. The final model included a temporal and a spatial component. The temporal trend consisted of second order polynomials in time plus a seasonality component, while the spatial trend was formed by second order polynomials of the coordinates plus the thin plate smoothing splines. The AGDDs of S. japonicum in 2003 and 2006 and their difference were calculated. The temperatures at the 39 locations showed an increasing temporal trend and seasonality with periodicities of 12, 6 and 3 months. The predicted AGDDs increased gradually from north to south in both 2003 and 2006. The increase in AGDD was particularly pronounced in the southern part of the study area. Our results suggest that alterations in the transmission intensity of S. japonicum in south Jiangsu will be more pronounced than in the northern part of the province. Fifth, we further assessed the potential impact of climate change on the distribution of O.hupensis via a spatially-explicit analytical approach. We employed two 30-year composite datasets comprising average monthly temperatures collected at 623 meteorological stations throughout China, spanning the periods 1961-1990 and 1971-2000. Temperature changes were assessed spatially between the 1960s and the 1990s for January, as this is the critical month for survival of O. hupensis. Our results show that the mean January temperatures increased at 590 stations (94.7%), and that China’s average January temperature in the 1990s was 0.96°C higher than 30 years earlier. The historical 0-1°C January isotherm, which has been considered the approximate northern limit of S. japonicum transmission, has shifted from 33°15’ N to 33°41’ N, expanding the potential transmission area by 41,335 km2. This translates to an estimated additional 21 million people at risk of schistosomiasis. Two lakes that form part of the SNWT project are located in this new potential transmission area, namely Hongze and Baima. Finally, we applied GIS/RS techniques to predict potentially new snail habitats around the lakes of Hongze and Baima, as well as Gaoyou lake, which is considered as a habitat where O. hupensis could re-emerge. A model based on flooding areas, NDVI and a wetness index extracted from Landsat images was developed to predict the snail habitats at a small scale. A total of 163.6 km2 of potential O. hupensis habitats were predicted around the three study lakes. In conclusion, our work suggests that global warming and a major water-resource development project could impact on the distribution of S. japonicum and its intermediate host snail in China and demonstrates that the combination of GIS, RS and Bayesian spatial statistical methods is a powerful approach in estimating their extent. The predictions can serve as a basis for health policy makers and disease control managers, and can be of use in the establishment and running of schistosomiasis surveillance systems. It is further suggested that an efficient early warning system should be set up in potential new endemic areas to monitor subtle changes in snail habitats due to climate change and major ecological transformations, and to assure the early detection of emerging and re-emerging schistosomiasis

WILD BIRDS AND EMERGING DISEASES: MODELING AVIAN INFLUENZA TRANSMISSION RISK BETWEEN DOMESTIC AND WILD BIRDS IN CHINA

Emerging infectious diseases in wildlife have become a growing concern to human health and biological systems with more than 75 percent of known emerging pathogens being transmissible from animals to humans. Highly pathogenic avian influenza (HPAI) H5N1 has caused major global concern over a potential pandemic and since its emergence in 1996 has become the longest persisting HPAI virus in history. HPAI viruses are generally restricted to domestic poultry populations, however, their origins are found in wild bird reservoirs (Anatidae waterfowl) in a low-pathogenic or non-lethal form. Understanding the spatial and temporal interface between wild and domestic populations is fundamental to taking action against the virus, yet this information is lacking. My dissertation takes two approaches to increase our understanding of wild bird and H5N1 transmission. The first includes a field component to track the migratory patterns of bar-headed geese (Anser indicus) and ruddy shelduck (Tadorna ferruginea) from the large H5N1 outbreak at Qinghai Lake, China. The satellite telemetry study revealed a new migratory connection between Qinghai Lake and outbreak regions in Mongolia, and provided ecological data that supplements phylogenetic analyses of virus movement. The second component of my dissertation research took a modeling approach to identify areas of high transmission risk between domestic poultry and wild waterfowl in China, the epicenter of H5N1. This effort required the development of spatial models for both the poultry and wild waterfowl species of China. Using multivariate regression and AIC to determine statistical relationships between poultry census data and remotely-sensed environmental predictors, I generated spatially explicit distribution models for China's three main poultry species: chickens, ducks, and geese. I then developed spatially explicit breeding and wintering season models of presence-absence, abundance, and H5N1 prevalence for each of China's 42 Anatidae waterfowl species. The poultry and waterfowl datasets were used as the main inputs for the transmission risk models. Distinct patterns in both the spatial and temporal distributions of H5N1 risk was observed in the model predictions. All models included estimates of uncertainty, and sensitivity analyses were performed for the risk models