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occurrence_clean_updated_diagnostics_checked.csv (358.21 kB)

Japanese encephalitis virus infection occurrence dataset 1935-2015

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posted on 2024-04-22, 04:25 authored by Freya ShearerFreya Shearer, Joshua Longbottom, Tehmina Bharucha, Annie Browne, David M. Pigott, Nick Golding, Catherine Moyes, Simon I. Hay

A database of locations where at least one symptomatic human infection of Japanese encephalitis virus was reported in any given year from 1935 to 2015, assembled from a variety of sources. Data were collated from online sources by the automated HealthMap system. HealthMap alerts were collated for the years from 2006 to 2015 and manually checked for validity, which resulted in the inclusion of data from 800 alerts. Online infectious disease reporting system ProMED or Program for Monitoring Emerging Diseases was also searched from 1994 (when the program was established) through to 2007 for reports of Japanese encephalitis, which returned 135 records. Thereafter it was assumed that ProMED reports were captured by the HealthMap system.

To collate data from peer-reviewed literature, ISI Web of Science and PubMed were searched using the term ‘Japanese encephalitis’ for all records up to July 1st 2015. The article abstracts were reviewed and the full text was obtained for those potentially containing geographical information on Japanese encephalitis virus infection in humans (979 articles).

Information regarding the site of infection of all reported Japanese encephalitis virus infections in humans was extracted from each article or report. Each reported site of infection was assigned coordinates in decimal degrees using a combination of information from the article or report and online gazetteers such as Google Earth, OpenStreetMap and Geonames. Multiple cases of Japanese encephalitis reported in the same location (i.e. same 5×5 km grid square) within the same calendar year, were recorded as a single occurrence. Only the longitude and latitude were recorded for locations smaller than 5×5 km in area (points). Areas larger than this (polygons) were linked to a shapefile either from the Food and Agricultural Organization, for first and second order administrative units (such as a province or district), or from Global Administrative Areas, for third order administrative units (such as a county or municipality).

Detailed information on the method used to diagnose each reported Japanese encephalitis virus infection were also extracted, where available. Diagnostic methods were classified into four confirmatory levels (1,2,3, or 4, with 1 = highest level of diagnostic confidence). Each occurrence record was then assigned a diagnostic confirmatory level. Records representing reported cases of Japanese encephalitis where the diagnostic test used was not specified were assigned level 5. For further details on diagnostic confidence levels see: 10.1016/j.ijid.2020.03.039.

Infections based on serological evidence in asymptomatic individuals were not included in the database due to the uncertainty regarding the time and site of infection and the person’s Japanese encephalitis vaccination history.

The final dataset contains a total of 3,424 Japanese encephalitis occurrence records, consisting of 2,074 point locations and 1,350 polygons.

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