New herpes database goes on-line

Contact: Shelley Thompson, sthompson@lanl.gov, (505) 665-7778 (02-012)

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LOS ALAMOS, N.M., Feb. 14, 2002 -- In an ongoing effort to aid in the search for cures and vaccines for sexually transmitted diseases, the Department of Energy’s Los Alamos National Laboratory released a publicly available Web database containing the Human herpesvirus 2 genomic sequence.

“The Sexually Transmitted Disease Genome Sequence Database (STDGEN) is a database developed to aid in the analysis of genomic sequences from sexually transmitted infectious agents,” said Thomas Brettin, project leader at Los Alamos. “Genomic sequences, like those in this database, have the potential to unlock the medical mysteries of pathogenic bacteria, viruses and parasites.”

In November 2001, the Los Alamos database team added the sequence of the Human herpesvirus 2, or HSV-2, the cause of most genital herpes cases, to the database. Earlier in 2001, the team entered the sequence of the herpes virus (Human herpesvirus 1) that causes most “cold sores” into STDGEN.

According to Penny Hitchcock, a Bioscience Division resource manager at Los Alamos and former chief of the Sexually Transmitted Diseases Branch for the National Institute of Allergy and Infectious Diseases, oral herpes, or cold sores, are quite common, and it is estimated that one of five Americans has genital herpes. These lifetime infections occur in different parts of the body and cause sores that often vary in severity and frequency of recurrence. Most people with genital herpes have silent infections or mild disease and do not know they are infected. Genital herpes can be unknowingly transmitted to partners and unborn babies, in the case of women who become infected during pregnancy. In addition to the pain and embarrassment of the infections, genital herpes has been a driving force in the AIDS epidemic. The sores of genital herpes increase the risk of HIV infection in two ways: HIV infects the inflammatory cells that are present near the sores, and people who have both genital herpes and HIV infection shed HIV from the genital sores.

“By translating the gene sequences of these organisms into protein sequences and making comparisons between related organisms, scientists hope to understand how organisms establish infection, why diseases caused by similar organisms are different and how to develop biomedical tools such as vaccines, microbicides, therapeutics and diagnostics that can be used to prevent and control these diseases,” said Brettin.

Los Alamos scientists received the HSV-2 genome sequence, originally determined at the McGeoch Laboratory, and translated it into protein sequences. Brettin’s team also performed structural and functional analysis on the sequences to determine potential biological functions of gene products, or proteins, and entered this information into the STDGEN database to be used by the herpes research community.

The STDGEN database provides the ability to search the database information with several search tools, each with different characteristics. The search tools range from one that allows asking simple questions across different information fields to one that searches protein sequences for sophisticated amino acid patterns. By performing special searches, the database reveals molecular differences and similarities among the viruses. Scientists can then conduct laboratory experiments to determine if the predictions about protein function are valid.

The database team continually adds to the contents of the database. Future additions to the herpes section of STDGEN will include genomic sequences of related herpes viruses that cause other serious diseases, such as infectious mononucleosis and Kaposi’s sarcoma, a type of cancer associated with herpes.

The STDGEN project is a continuation of a project started by Los Alamos in the early eighties. Los Alamos scientists created the GenBank database that now currently resides at the National Institutes of Health. The GenBank database provides access within the scientific community to the most up to date and comprehensive DNA sequence information.

After creating GenBank, Los Alamos began the HIV and human papalomavirus – one of the primary causes of cervical cancer – databases. When scientists first created these databases they distributed data in large notebooks to interested parties. Later, Los Alamos decided to make this information available on the Web so it would be more convenient and accessible. In 1998, Brettin expanded this idea and developed the software for STDGEN and included tools for searching the database and studying in depth the genomic sequences of STD causing organisms.

These specialized databases are an expansion of the human papillomavirus project funded by the Sexually Transmitted Diseases Branch of the Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda Maryland.

STDGEN can be found on the Web at www.stdgen.lanl.gov online.

Los Alamos National Laboratory is operated by the University of California for the National Nuclear Security Administration (NNSA) of the U.S. Department of Energy and works in partnership with NNSA's Sandia and Lawrence Livermore national laboratories to support NNSA in its mission.

Los Alamos enhances global security by ensuring safety and confidence in the U.S. nuclear stockpile, developing technologies to reduce threats from weapons of mass destruction and improving the environmental and nuclear materials legacy of the cold war. Los Alamos' capabilities assist the nation in addressing energy, environment, infrastructure and biological security problems.