February 15, 2011 (Vol. 31, No. 4)

Editor’s Note

 It was 30 years ago in 1981 that the first known case of acquired immune deficiency syndrome (AIDS) was definitively diagnosed. According to last year’s “UNAIDS Report on the Global AIDS Epidemic”, 31.4-35.3 million people around the world were living with AIDS in 2009. The UNAIDS study also estimates that over 25 million people have died of AIDS-related diseases since 1981.

This issue’s article commemorating GEN’s 30th anniversary is reprinted from February 1985. It recounts how two laboratories, for the first time, independently sequenced the virus believed to cause AIDS. The finding opened the door to the development of new AIDS diagnostics and therapeutic strategies for helping to alleviate the suffering of those afflicted with AIDS.

The AIDS story is the latest example of our decision to reprint an article from one of GEN’s early issues in each issue in 2011. All these stories demonstrate a particular significance and relevance for the life science research community.

John Sterling, Editor in Chief

“As Seen in GEN” Volume 5, Number 2, February 1985

U.S., French Teams Map AIDS-Linked Virus

By Joan Stephenson Graf

Two research groups, one in the United States and the other in France, revealed that they have independently succeeded in sequencing the virus believed to cause acquired immune deficiency syndrome (AIDS). The two reports apparently confirm that the two viruses linked with AIDS, HTLV-III and LAV are, as scientists believed, the same virus.

The accomplishment represents a crucial bench mark in research on the deadly disease, helping researchers to understand how the virus functions and to develop diagnostic tests and a vaccine against the virus.

Moreover, the HTLV family of viruses may represent a new class of retroviruses that are important human pathogens. According to Dr. Mark Pearson of E.I. du Pont de Nemours, “These viruses appear to represent a new type of virus. Other members of this new virus family may be involved in other chronic diseases. We are just beginning to understand these agents and their role in human disease,” he said.

The analysis of the HTLV-III virus was initiated and coordinated by Drs. Robert Gallo and Flossie Wong-Staal of the National Cancer Institute; four other laboratories collaborated with the NCI group, including a second laboratory at NCI (under the direction of Dr. Takis Papas), a team at Harvard Medical School and Dana-Farber Cancer Institute (led by Dr. William Haseltine), a group at E.I. du Pont de Nemours & Co. in Wilmington, Del. (directed by Dr. Pearson), and a team at Centocor in Malvern, Pa. (led by Dr. Nancy Chang). The LAV virus was sequenced by a group of scientists at the Pasteur Institute in Paris, including Drs. Simon Wain-Hobson, Pierre Sonigo, Olivier Danos, Stewart Cole and Marc Alizon.

Knowing the exact sequence will help AIDS research in a number of ways. The protein or nucleic acid products encoded by the viral genome can be synthesized for research and for medical applications. “It will facilitate any recombinant DNA strategy, because it provides information about how and where to cut and splice,” Dr. Wong-Staal told GEN.

“It should bring more people into the field, because now we can make proteins and fragments of proteins,” said Dr. Gallo. Furthermore, the ability to work with selected portions of the pathogen rather than whole virus makes it possible for researchers to conduct research without fear of contracting the fatal ailment.

Diagnostic Tests

“One major medical implication [of the sequencing of the virus] is that now we can proceed with much greater precision to make the reagents necessary for unambiguous diagnostic tests,” said Dr. William Haseltine. There appears to be some ambiguity in the current generation of diagnostic tests, leading to false positives and negatives, he said. The sequencing work, however, makes possible the development of a much more precise series of tools to be used not only for screening blood but also for diagnosis in individuals, he added.

According to a statement issued by the NCI, the knowledge of the viral genome is already being used to develop methods for detection of the virus in blood samples. Several companies, including Genentech and Chiron (both of whom are said to be close to mapping the genome of the virus) are racing to develop blood-screening tests.

The sequencing work also represents a crucial point in the long process of developing a preventive vaccine, and perhaps, therapy to alleviate the symptoms of the disease in individuals who become infected with the virus.

The mapping of the viral genome will provide a set of tools for the design of a series of “prototype” vaccines, Dr. Haseltine said.

“We can now take various genes out—particularly the envelope gene, which we suspect will be crucial in making an active vaccine—and manipulate them via recombinant techniques into appropriate vectors that we think will be good for vaccines.”

Although he thinks it unlikely that infected individuals can be cleared of the disease, Dr. Haseltine suggested that the sequencing of the virus has laid the groundwork for the development of therapeutics to reduce the severity of the symptoms.

“In the area of therapy, it offers very detailed information about the structure of the viral proteases, the virus reverse transcriptase, the virus envelope genes—all of which are potential targets for therapy,” he said. “If you can inhibit active virus replication, you may go some way toward alleviating the symptoms of virus infection, perhaps by preventing people who are asymptomatic from becoming symptomatic, or by alleviating the severity of the disease in the symptomatic individual.”

A New Virus

HTLV-III, the presumptive AIDS virus, belongs to the family of retroviruses known as human T-cell leukemia-lymphotropic viruses (HTLV). This group of agents includes HTLV-I, which is strongly associated with an adult form of leukemia-lymphoma that is uncommon in the United States but found more frequently in other parts of the world (including Japan, the Caribbean, parts of Africa, and South and Central America); and HTLV-II, which was isolated from a patient with hairy cell leukemia. The American groups report that while the HTLV-III virus shares some important similarities with other retroviruses—particularly the other two known HTLV viruses (as well as bovine leukemia virus)—HTLV-III has some unique properties. They conclude that HTLV-III is a new virus, rather than a virus that arose by small changes in known viruses already present in the population.

Dr. Wong-Staal of NCI said, “Although we recognize several key features of the virus structure from studies of related viruses, other features of the virus are new and unique to this virus. We speculate that some of these unusual features may be involved with mechanisms of disease.”

Dr. Haseltine described the structure of the HTLV-III virus as “surprising”. “It is similar in many respects, and in fundamental respects, to other retroviruses—particularly the human leukemia viruses and a close relative, the bovine leukemia virus,” he said.

Like other retroviruses, HTLV-III is an RNA virus that contains a set of proteins (core proteins) that surround the RNA, uses a polymerase (reverse transcriptase) to convert RNA to DNA as part of its life cycle, and is surrounded by an outer envelope. However, while the organization and structure of the core proteins and polymerase genes generally resemble those features in other retroviruses (particularly HTLV-I and HTLV-II), the organization of the key envelope genes of HTLV-III appears to be unique.

Dr. Lee Ratner, a researcher at NCI and the first author on the American group’s report in the January 24 issue of Nature, said that the envelope gene “was not where we expected it to be” and that the gene for the envelope protein is much larger than similar genes in other retroviruses.

A major surprise came from an analysis of a genetic region which is “bi-functional, encoding both an envelope gene and a gene called lor we had previously recognized in HTLV-I, HTLV-II, and bovine leukemia virus,” Dr. Haseltine told GEN. “The lor gene of the virus overlaps the envelope gene; one genetic region [of the HTLV-III virus] has two distinct functions in this virus—it encodes both the envelope and lor proteins.” In the human leukemia viruses, the envelope and lor genes are separate genes.

Researchers believe the lor gene is important for the growth of the virus itself, as well as for determining the effects of virus infection on the target cells. Both the human leukemia viruses and the AIDS virus infect the same kind of immune cells—the T-4 population of T cells (helper T cells). The outcomes of the infections are markedly different; while the human leukemia virus immortalizes the T cells and cause uncontrolled growth, the AIDS virus kills these cells and causes the failure of the immune system that characterizes AIDS.

“We’re interested in how the virus works, why it kills the same cells that the leukemia viruses immortalize,” said Dr. Wong-Staal.

“There’s something quite specific and interesting about the killing mechanism that has to be understood,” Dr. Haseltine said. He says that the action of the lor gene might be responsible for determining the different effects of the viruses in the HTLV family on the same type of cell. If this is the case, then a detailed analysis of how the gene products work could be important in the development of new therapeutic approaches for treatment of AIDS infections.

Unique Genetic Regions

There are at least two regions of the HTLV-III virus—called sor and 3’ orf—that have no direct counterpart in any other retrovirus studied to date. According to the Nature report, sor may be a remnant of a former envelope gene; 3’ orf may not be a gene at all, since only one of the two HTLV-III isolates that were sequenced contained such a region.

The nucleotide sequences of two isolates studied by the American group differed by about 1 percent, Dr. Haseltine told GEN. Similarly, the genetic analysis of the LAV isolate by the French group—which appears in the January issue of Cell—differed from either of the American sequences by about 1 percent.

“I think the fundamental thing is that they [HTLV-III and the LAV] are the same agent—there’s no doubt any longer,” said Dr. Haseltine.

Chiron Corporation has analyzed a virus known as ARV (AIDS-Related Virus) and expects to publish their results in the February 1 issue of Science. Dr. Haseltine said, based on discussions he has had with members of the Chiron group, that the ARV is yet another isolate of the HTLV-III virus.

In related work, the American team claims that the HTLV-III virus, like the other HTLV viruses, alters cells by affecting the mechanism by which genes are transcribed, a phenomenon called trans-acting transcriptional regulation (TAT). They suggest that the common structural and functional features of the HTLV viruses—the presence of the lor gene and the TAT phenomenon—set the HTLV family of viruses apart from other retroviruses.

8,000 AIDS Cases

Nearly 8,000 cases of AIDS have been reported in the United States since 1981, and more than 45 percent of the victims have died.

Although government agencies and the scientific community have been criticized—particularly by members of the major risk group, male homosexuals—for not gearing up to study the problem quickly enough, many investigators in the field now feel that research has progressed at an astonishing pace.

“The whole series of experiments that have been done so far have been accomplished in record time—from first recognition of the HTLV-III virus to complete nucleotide sequencing in less than nine months,” Dr. Haseltine said.

“This particular effort represents a very good cooperation among a number of research groups that one might otherwise think would be competitive—and I think it represents the recognition that AIDS is a very important problem that needs an immediate solution,” he added.

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