A Hepatitis A database has shown promise, and with improvements could be used at earlier stages of international outbreaks, according to researchers.
The team assessed usefulness of the dataset for geographical annotation, backtracing and outbreak detection and results were published in the Eurosurveillance journal.
Hepatitis A virus Network (HAVNet) is an international laboratory network set up in 2010 for sharing sequences and corresponding metadata on hepatitis A virus in an online database.
Hepatitis A virus (HAV) causes acute liver disease and is transmitted through ingestion of contaminated food and water or through direct contact with a contagious person. Countries producing and exporting fruit, vegetables and shellfish may have a higher level of HAV endemicity than those importing the products.
Due to the long incubation period for hepatitis A of 15-50 days, linking and traceback of foodborne clusters or outbreaks of HAV are not straightforward. The virus is stable in the environment and infectious dose is low. It is also preserved in frozen, ready-to-eat products which may be shipped globally.
A Hepatitis A outbreak declared over recently in Sweden affected 20 people and was linked to frozen imported strawberries from Poland.
European authorities are still investigating 62 hepatitis A cases reported by eight EU countries with the latest in mid-June 2018. Cases in Denmark, France, Germany, Ireland, Netherlands, Spain, Sweden and the United Kingdom are infected with one of two HAV genotype IA strains.
Since July and until the end of August, Austria has recorded nine hepatitis A cases with the source unknown. It is not believed that these cases are connected to the multi-country EU outbreak.
A download of the HAVNet dataset in February 2017 was used for the analyses, containing 9,211 reports, with 9,783 sequences (572 reports reported two sequences, from two different genomic regions), of which 2,426 reports were submitted by 18 HAVNet members and 6,785 were retrieved from GenBank.
The 2,426 reports from HAVNet members were evaluated for epidemiological data. Of these, 972 were reported with a possible source of infection and 508 of these had travel to an endemic country, and 77 recorded a possible foodborne source, of which 16 reported shellfish, 18 fresh or frozen fruit, and 43 other or unknown food.
Researchers said in many reports, essential metadata are missing and while some parts of the world are well-covered for reports and sequences other parts are missing.
“Analysis of the current global dataset of sequence data for HAV shows that the HAVNet database is promising for source tracking; however, improvements in data quality are necessary to cover gaps regarding essential metadata and to enable optimal and timely use of such data in outbreak studies,” they said.
For HAVNet reports with complete sampling dates and reported after 2010 the median reporting lag for the 850 included reports was 94 days (min = 0 days, max = 1,282 days), with large differences per country and no trend over the years.
“With the current lag times for reporting, the database is able to serve as an outbreak detection tool for frozen foods with long shelf lives. For fresh produce, however, timeliness requires improvement, as, combined with the long incubation period for HAV, it is outside the actionable range,” said researchers.
However, data collected within the network has supported detection and source-tracing of several international foodborne outbreaks.
The password protected database is used on a give-and-take basis which involves signing a confidentiality agreement.
Researchers said if the HAVNet database can be further improved, it could make use of other sources, or be used at earlier stages of international outbreaks.
“To optimize public health profit, the HAV community is encouraged to expand its genome sequencing efforts, in terms of genome coverage, metadata provision and timely sharing of information,” they added.
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