Overall: Understand the epidemic and unresolved spatial and temporal trends and patterns of HPAI outbreaks occurring

in Hong Kong from early 1997 in order to aid in HPAI surveillance and future control and prevention in the country. Specific objectives: Project 1: Spatial Epidemiology of Avian Influenza: Current Approaches and Methodological Issues

Objectives: Make a review of existing and newly developed tools for spatial analysis for avian influenza research.

Review the strength, limitations and ways to overcome such limitations of different spatial tools in avian influenza research

Project 2: The spatial and temporal magnitude of HPAI outbreaks: 1997-2011, Hong Kong

Objective: Description of the patterns and impacts of H5N1 outbreak in Hong Kong (1997 to 2011) over space and time using the visualization and exploratory techniques

Project 3: Space-Time cluster of HPAI outbreaks in Hong Kong, 1997-2011

Objective:

Further examination of the outcome of visualization of the outbreak locations for the purpose of their randomness

Ho = There is no cluster of cases in space

Project 4: Spatial and temporal trend of HPAI outbreaks: 1997-2011, Hong Kong.

Objectives: a. Analyze HPAI outbreak data in Hong Kong between 1997- 2011 for detection of particular trend b. Analyze HPAI viruses in Hong Kong between 1997- 2011 for detection of particular trend in genetic changes

a. Discuss any regional and seasonal variations in the general trend

Ho = There is no variation in the timescale of outbreak

b. Discuss any regional and seasonal variations in the general trend

Ho = There is no relation between genetic diversity of the virus with temporal and geographic diversity

Project 5: Ecological risk factors of HPAI in Hong Kong Objective: Spatial exposure measurement and quantify and/ or predict the nature of the association between spatially referenced outcome of interest.

Ho= Infection in sub district f (ecological determinants)

Project 6: Spatial risk mapping of HPAI outbreaks in Hong Kong

Objective: Identification of areas in the country that are at high vulnerability and risk to HPAI. The maps will help as important policy and decision tools towards better HPAI management and adaptation in the country.

Background, state-of-the-art and relevance Highly pathogenic avian influenza (HPAI) of subtype H5N1 virus was first reported on February 5, 2007 in Bangladesh. Since the epidemic wave in chickens, the country has attempted to restrain HPAI outbreaks through a range of control measures. As of 31 st May 2009, HPAI H5N1 virus has been isolated from 324 (273 commercial and 51 backyard) poultry farms in different areas of the country (www.mofl.gov.bd). The HPAI H5N1 virus struck 48 of Bangladeshs 64 districts (www.mofl.gov.bd). To date, in the country, only a 16month old baby has been reported to have H5N1 infection with no case fatality. WHO confirmed that case of Bangladesh raises the global H5N1 human cases count to 383 cases with 241deaths (May, 2008 http://www.cidrap.umn.edu). The outbreaks of an infectious disease concentrated in a zone are termed as clusters. Significant clustering of outbreaks were found for many diseases like SARS(Lai et al., 2004), FMD (Ortiz-Pelaez., 2006), west Nile virus infection (Marilyn et al ., 2004), Bovine Spongiform Encephalopathy (Stevenson et al., 2000; Doherr et al., 2002), Brucellosis (Fosgate et al., 2002) and HPAI (Pfeiffer et al., 2007). This trend can be observed spatially and temporally. The clusters indicate the point and local source of exposure (Marilyn et al., 2004). Perhaps some factors associated with the disease outbreak are geographically more intense in the clustered zone. A study dealing with Thai HPAI outbreaks hypothesized that human activity and densely populated poultry area may have played a role for the number of HPAI outbreaks. Owing to a less strong association found there in national level, a strong urge was made to follow up with a local level analysis for hotspots (cluster) of the HPAI outbreaks (Gilbert et al., 2006).

The pattern of the HPAI outbreaks in Hong Kong has not been systematically evaluated so far. It is very important to understand the trend of the disease from the perspective of the

time and of the space. For effective prevention, control and proper allocation of resources, it is crucial to understand the spatial and temporal patterns of the diseases occurrence and distribution of risk factors for introduction, spread and containment of the outbreaks. The purpose of our proposed study is to evaluate spatial clusters and their dependence on ecological risk factors irrespective of time and space. Moreover, we aim to model risk based surveillance programme including sampling techniques for Hong Kong. Research plan and methods Incidence Data We will use the number of poultry cases reported by the Department of Livestock Services (DLS), Bangladesh to OIE from 2007 through our study period. Case data, were acquired through DLS personnel, which include clinical disease with laboratory confirmation. Data for cases will be downloaded from the OIE website (http://www.oie.int/downld/AVIAN%20INFLUENZA/A_AI-Asia.htm ). Date of outbreak, coordinate data, number of animal died, types of farming are available in this report. District wise poultry holding number and poultry number is available from Bangladesh Bureau of Statistics (BBS). Latest census data will be used.

Geographic and determinant data: For administrative purpose Hong Kong is divided into 18 geographic districts. The district level digital map of Hong Kong is available and will be used for this study that followed North American 1927(GCS Assumed Geographic) coordinate system. Species, types of production system, geographic location (latitude and longitude) and timing of individual case is available. Moreover, wetland, vegetation, temperature, humidity rainfall and land use data and human population density is also available. Other variables which are biologically relevant will also be considered for the study.

Activities under objective 1:

For the review, we will include full length articles describing the distribution, surveillance, distribution and control, risk estimation or prediction and risk factor analysis using spatial epidemiological tools.

Search strategy: Pub med (1997 to 2011) and Hong Kong University Library (1997 to 2011).

Search Key: Epidemiology of Avian Influenza, spatial analysis of avian influenza, Spatial Epidemiology of avian influenza, descriptive epidemiology of avian influenza.

Expected outcome: The project will end up with a review article addressing the spatial epidemiologic tools their current uses and future possibilities in HPAI research.

Activities under objective 2: We will develop an epidemic curve with three days moving average to reduce the noise of the data and will compare it with a normal epidemic curve (Ordinary Histogram). 3D surface map/ scatter plot will be developed where we will simply plot number of cases on the z axis as a function of spatial locations in the x, y plane to describe the spatial distribution of the disease. To visualize H5N1 disease spread, we will plot the incidence by district and by year using the spatial statistics tools of ArcGIS. Instantaneous hazards curve will also be developed for showing the progression of the confirmed H5N1 outbreaks. For time to individual sub districts experiencing an outbreak during the epidemic of 18 different geographic districts will be demonstrated by Kaplan Meier survivals function. These analyses will provide some interesting insight into the infection process because they will consider the number of sub districts, not only the case data alone. It will give us some idea regarding the rapidness of spread over geographical location. We will also measure the persistence of outbreak by the cumulative number of months with reported outbreaks in particular sub district and develop exploratory map. Description of the control measures will be described by the spatial buffering and descriptive statistics. Finally, we will try to discuss the epidemic as a whole, and its causal pathway. Expected outcome: A mimic picture of the HPAI outbreak in Hong Kong with special reference to space and time

Activities under objective 3:

Spatial patterns analysis: It is always considered important to use multiple techniques to check the clustering of the events. To identify clusters of infected district from vector data a two-step approach will be followed. In the first step we shall calculate the global Morans I for the vector data and K-function for the point data to check the presence of

cluster in our risk maps. Both methods results in a global measure of spatial autocorrelation and can only state the presence of cluster without identification of the specific location. In the second step, we shall estimate the Local Indicators for Spatial Association (LISA), which is the local version of Morans I to identify the exact location of the cluster. To reconfirm the location of the clusters and type (Primary or secondary) we also examine the whole process using scan statistics for point source data.

Expected outcome: An understanding on the clustering of the HPAI outbreaks in Hong Kong. Besides, the project will explore whether there is any variation of spatial clusters when we use the point source data and vector data from the same outbreak.

Activities under objective 4: a. We will use temporal trend analysis to detect the presence and evaluate the significance of seasonal and temporal trend in the occurrence of HPAI in Hong Kong. We wish to explore the spatial and temporal dynamics in this project. b. We will perform phylogeographic analysis to detect any trend in genetic diversity. Expected outcome: Evidences of variation in spatial and temporal occurrences of HPAI outbreaks in Hong Kong and evolution of the virus. Activities under objective 5: We will try to measure and quantify any association present between the event of AIs and ecological variables. Binary Logistic regression will be the tool to test association. Odds ratio (OR) and p value with 95% confidence interval will be calculated. For model building we will use backward LR (p<.05 significant level) approach. Logistic model will be tested by using the Hosmer-Lemeshow goodness of fit and best model will be selected on the basis of Akaike information criterion (AIC). We will also use the discriminant analysis in this project as alternative tool for examining the association. Possible list for the explanatory variables: Population density, poultry density, wetlands, water body, biosecurity, presence of risk way, migratory birds, precipitations, humidity, temperature, precipitation, vegetation and topography etc. We will use census data and data extracted from the remote sensing to adjust the resolution of the data sets. Expected outcome: Determined ecological risk factors and calculate modifiable portion (if modifiable) Activities under objective 6:

We will use multiple sources of data from previous projects to create a Bayesian risk map. Later we wish to model a surveillance programme using multilevel modeling for sampling scheme and for the prediction of future outbreak. In other words, we wish to propose a risk based surveillance model for Hong Kong. Before we consider the explored patterns for the model we would also adjust the patterns for different fit falls of current reporting system. For example, we will check the correlations between the clustered zone and public awareness regarding HPAI in a particular zone. Expected outcome: Detected high risk zones for HPAI outbreaks in Hong Kong enabling prioritizing the allocation of resources for undertaking a better HPAI surveillance and control programme in the country Timetable (indicate the most important milestones) Year Plan (1st year) (March to December 2012)
Jan PhD plan ( To be submitted) Start up seminar Project-1 (Literature Review) Scientific Writing (A) Introduction course for PhD Students PhD course in spatial epidemiology Data management Project -2 (Exploratory and descriptive) Vet Epidemiology-1 Vet Epidemiology-2 Vet Epidemiology-3 Year Plan (2nd year) (January to December 2013) Jan Project- 3 (Cluster analysis) Data Management GIS Course #Bio informatics in micro biology Project- 5(Ecological determinants) Remote sensing Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec X X X X Including manuscript preparation X Substitute course taken Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Remarks X X X X X X X

28 Including Manuscript preparation 21-24 15-19 22-26

Including Manuscript preparation

31

1-4

2 5-9

13 16-20

18

X X X

Including manuscript preparation

Year Plan ( Final Year) (Jan2014 to May 2015) (Adjusted)

Jan Feb Mar Apr May JunAug Sep Oct Nov Dec Jan,12 Feb12 Mar12 Apr12 May12

Avek

Project- 4 (Phylogeography and trend) #Infection Microbiology Conference Project -6 +4 (trend analysis + risk mapping) Conference

Including manuscript preparation

X X

repara tion

Including manuscript preparation X

Thesis preparation Thesis submission

June 6, 2015