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TranStat

The key to controlling a pandemic is early detection, containment, and mitigation. The TranStat tool was developed to enable field personnel and researchers to enter and revise data from local outbreaks. From these data TranStat provides a means of testing for the presence of human-to-human (or animal-to-animal) transmission. If this transmission is detected, estimates of the household-specific and neighborhood-specific secondary attack rates and local reproductive number are provided.

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The algorithm for TranStat Version 0.1, the first release of the tool to the general research community, was written by researchers at the University of Washington (UW) and Fred Hutchinson Cancer Research Center (FHCRC); the user interface was designed as a collaboration between the UW, FHCRC and RTI International and was implemented using Java by RTI International.

We encourage your comments so we can improve future versions

The TranStat version 0.1 can be run on Windows platforms and later versions will be able to run on any platform, including Linux. Users will need to install the Java Runtime Environment version 6 that can be downloaded from the Java Sun site. Users need to download and install file: 'jre-6u3-windows-i586-p.exe' or file 'jdk-6u3-windows-i586-p.exe'. Once Java has been installed, unzip the TranStat.zip file to file system and execute (double-click at) the TranStat.jar file.

User's Manual


TranStat is based on research published in two articles:

Yang Y, Longini IM Jr, Halloran ME. (2007)
A resampling-base test to detect person-to-person transmission of infectious disease.
Ann Appl Statist. 2007;1(1):211-28. doi:10.1214/07-aoas105.

Abstract

Early detection of person-to-person transmission of emerging infectious diseases such as avian influenza is crucial for containing pandemics. We developed a simple permutation test and its refined version for this purpose. A simulation study shows that the refined permutation test is as powerful as or outcompetes the conventional test built on asymptotic theory, especially when the sample size is small. In addition, our resampling methods can be applied to a broad range of problems where an asymptotic test is not available or fails. We also found that decent statistical power could be attained with just a small number of cases, if the disease is moderately transmissible between humans.

Online Link: here

Yang Y, Halloran ME, Sugimoto J, Longini, Jr IM. (2007)
Detecting human-to-human transmission of avian influenza A (H5N1).
Emerg Infect Dis. Volume 13, Number 9-September 2007

Abstract

Highly pathogenic avian influenza A (HPAI) subtype H5N1 has caused family case clusters, mostly in Southeast Asia, that could be due to human-to-human transmission. Should this virus, or another zoonotic influenza virus, gain the ability of sustained human-to-human transmission, an influenza pandemic could result. We used statistical methods to test whether observed clusters of HPAI (H5N1) illnesses in families in northern Sumatra, Indonesia, and eastern Turkey were due to human-to-human transmission. Given that human-to-human transmission occurs, we estimate the infection secondary attack rates (SARs) and the local basic reproductive number, R0. We find statistical evidence of human-to-human transmission (p = 0.009) in Sumatra but not in Turkey (p = 0.114). For Sumatra, the estimated household SAR was 29% (95% confidence interval [CI] 15% - 51%). The estimated lower limit on the local R0 was 1.14 (95% CI 0.61 - 2.14). Effective HPAI (H5N1) surveillance, containment response, and field evaluation are essential to monitor and contain potential pandemic strains.

CDC Link: here.