Usability of the international HAVNet hepatitis A virus database for geographical annotation, backtracing and outbreak detection.
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Authors
Kroneman, Anneliesde Sousa, Rita
Verhoef, Linda
Koopmans, Marion P G
Vennema, Harry
On Behalf Of The HAVNet Network
Type
ArticleLanguage
en
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Usability of the international HAVNet hepatitis A virus database for geographical annotation, backtracing and outbreak detection.Published in
Euro Surveill 2018; 23(37):pii.1700802Publiekssamenvatting
BackgroundHAVNet is an international laboratory network sharing sequences and corresponding metadata on hepatitis A virus in an online database. Aim: We give an overview of the epidemiological and genetic data and assess the usability of the present dataset for geographical annotation, backtracing and outbreak detection. Methods: A descriptive analysis was performed on the timeliness, completeness, epidemiological data and geographic coverage of the dataset. Length and genomic region of the sequences were reviewed as well as the numerical and geographical distribution of the genotypes. The geographical signal in the sequences was assessed based on a short common nt stretch using a 100% identity analysis. Results: The 9,211 reports were heterogeneous for completeness and timeliness, and for length and genomic region of the sequences. Some parts of the world were not represented by the sequences. Geographical differences in prevalence of HAV genotypes described previously could be confirmed with this dataset and for a third (1,075/3,124) of the included sequences, 100% identity of the short common sequence coincided with an identical country of origin. Conclusion: Analysis of a subset of short, shared sequences indicates that a geographical annotation on the level of individual countries is possible with the HAVNet data. If the current incompleteness and heterogeneity of the data can be improved on, HAVNet could become very useful as a worldwide reference set for geographical annotation and for backtracing and outbreak detection.PMID
30229723ae974a485f413a2113503eed53cd6c53
10.2807/1560-7917.ES.2018.23.37.1700802
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- Creative Commons
Except where otherwise noted, this item's license is described as Archived with thanks to Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
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