Abstract
BackgroundIt is estimated that 15 to 20 million people are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). At present, there are more than 2,000 unique HTLV-1 isolate sequences published. A central database to aggregate sequence information from a range of epidemiological aspects including HTLV-1 infections, pathogenesis, origins, and evolutionary dynamics would be useful to scientists and physicians worldwide. Described here, we have developed a database that collects and annotates sequence data and can be accessed through a user-friendly search interface. The HTLV-1 Molecular Epidemiology Database website is available at http://htlv1db.bahia.fiocruz.br/.Methodology/Principal FindingsAll data was obtained from publications available at GenBank or through contact with the authors. The database was developed using Apache Webserver 2.1.6 and SGBD MySQL. The webpage interfaces were developed in HTML and sever-side scripting written in PHP. The HTLV-1 Molecular Epidemiology Database is hosted on the Gonçalo Moniz/FIOCRUZ Research Center server. There are currently 2,457 registered sequences with 2,024 (82.37%) of those sequences representing unique isolates. Of these sequences, 803 (39.67%) contain information about clinical status (TSP/HAM, 17.19%; ATL, 7.41%; asymptomatic, 12.89%; other diseases, 2.17%; and no information, 60.32%). Further, 7.26% of sequences contain information on patient gender while 5.23% of sequences provide the age of the patient.Conclusions/SignificanceThe HTLV-1 Molecular Epidemiology Database retrieves and stores annotated HTLV-1 proviral sequences from clinical, epidemiological, and geographical studies. The collected sequences and related information are now accessible on a publically available and user-friendly website. This open-access database will support clinical research and vaccine development related to viral genotype.
Highlights
Human T-cell lymphotropic virus type 1 (HTLV-1) is the first described human retrovirus and was isolated from a patient with cutaneous T-cell lymphoma [1]. It is the causative agent of tropical spastic paraparesis/human T-cell lymphotropic virus type 1 (HTLV-1)-associated myelopathy (TSP/HAM) [2,3], adult T-cell leukemia/lymphoma (ATLL) [4], and other inflammatory diseases such as HTLV-1-associated infectious dermatitis [5,6] and HTLV-1-associated uveitis (HAU) [7]
The HTLV-1 sequences and notes were taken directly from GenBank and submitted to the BLAST algorithm (Basic Local Alignment Search Tool) [18] in order to compare the information obtained from nucleotide sequences with those contained in the library or from the tool base itself
Of the 2,457 sequences stored in the HTLV-1 Molecular Epidemiology Database, 1,933 (78.67%) sequences represent unique isolates
Summary
Human T-cell lymphotropic virus type 1 (HTLV-1) is the first described human retrovirus and was isolated from a patient with cutaneous T-cell lymphoma [1]. It is estimated that approximately 15 to 20 million people worldwide are infected with HTLV-1 [10]. It is estimated that 15 to 20 million people are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). A central database to aggregate sequence information from a range of epidemiological aspects including HTLV-1 infections, pathogenesis, origins, and evolutionary dynamics would be useful to scientists and physicians worldwide. The HTLV-1 Molecular Epidemiology Database website is available at http://htlv1db.bahia.fiocruz.br/
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