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Usability of the international HAVNet hepatitis A virus database for geographical annotation, backtracing and outbreak detection

2018-09Journal article Open access
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dc.contributor.authorKroneman, A.
dc.contributor.authorde Sousa, R.
dc.contributor.authorVerhoef, L.
dc.contributor.authorKoopmans, M.P.G.
dc.contributor.authorVennema, H.
dc.contributor.authorOn Behalf Of The HAVNet Network
dc.date.accessioned2019-02-15T15:32:30Z
dc.date.available2019-02-15T15:32:30Z
dc.date.issued2018-09
dc.descriptionFree PMC Article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6144472/
dc.description.abstractBackground:HAVNet 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.pt_PT
dc.description.sponsorshipECDCpt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationEuro Surveill. 2018 Sep;23(37):pii=1700802. doi: 10.2807/1560-7917.ES.2018.23.37.1700802pt_PT
dc.identifier.doi10.2807/1560-7917.ES.2018.23.37.1700802pt_PT
dc.identifier.issn1560-7917
dc.identifier.urihttp://hdl.handle.net/10400.18/5834
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherEuropean Centre for Disease Prevention and Controlpt_PT
dc.relation.publisherversionhttps://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2018.23.37.1700802pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/pt_PT
dc.subjectCluster Analysispt_PT
dc.subjectDatabasept_PT
dc.subjectGenotypept_PT
dc.subjectHepatitis A Viruspt_PT
dc.subjectMolecular Typingpt_PT
dc.subjectInfecções Sistémicas e Zoonosespt_PT
dc.titleUsability of the international HAVNet hepatitis A virus database for geographical annotation, backtracing and outbreak detectionpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.issue37pt_PT
oaire.citation.startPage:pii=1700802pt_PT
oaire.citation.titleEurosurveillancept_PT
oaire.citation.volume23pt_PT
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT

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