“If we want to stop the HIV epidemic, then we must know the mechanisms by which HIV uses human sex to spread,” said principal investigator Davey Smith, MD, MAS, associate professor of medicine in UCSD’s Division of Infectious Diseases and in the Veterans Affairs San Diego Healthcare System, and director of the CFAR Viral Pathogenesis Core.

It is known that most HIV infections worldwide result from exposure to the HIV virus in semen, made up of seminal cells and the fluid around these calls, called seminal plasma. HIV virus particles contain RNA and exist in the plasma, while infected seminal cells contain HIV DNA.

Using a method of comparing genetic characteristics, called phylogenetic analysis, the researchers studied a group of men who had sexually transmitted their HIV virus to other men. Phylogenetic models allow researchers to estimate the dates of origin of various groups of viruses; in this way the team was able to determine the source of rapidly mutating HIV viruses by analyzing the viral sequences extracted from the blood and semen of HIV transmitting partners. The team found that recipients shared a more recent common ancestor with virus from the seminal plasma than with virus found in the seminal cells of their source partner.

“Until now, it had not been established whether HIV RNA or DNA is transmitted during sex,” said Smith. “By analyzing the genetic differences between these two forms and the virus that was ultimately transmitted to newly infected individuals we found that it was the HIV RNA form present in seminal plasma that was transmitted.”

“The findings from this study will help direct prevention strategies to address the virus in the seminal plasma,” Smith said. “By knowing the origin of the transmitted virus, scientists may be able to develop new vaccines, vaginal microbicides and drugs to prevent the spread of sexually transmitted HIV.”

Smith notes that because the study involved pairs of men who have sex with men, the findings do not comment directly on HIV transmission to women. “Since the vast majority of women are infected with HIV by exposure to the virus in semen, HIV RNA in the seminal plasma is the likely culprit, but this needs to be confirmed,” he said.

The results of this paper, “HIV and Tuberculosis Co-infection Among Hispanics in Southern California: An Increasing Health Disparity,” will appear in the February edition of the American Journal of Public Health.

“While the overall numbers are modest, our study shows that what used to be mostly a disease of white and black patients in San Diego is now largely a disease of Hispanics,” said Timothy Rodwell MD, PhD, MPH, associate physician/fellow in the Division of Global Public Health at UC San Diego. “This indicates that the benefits of prevention and treatment of TB and HIV over the last decade have been uneven in the different ethnic/racial groups in this region.”

HIV is a potent risk factor for TB disease. It increases the risk of latent TB infection reactivation, the rate of disease progression and the risk of new infections. TB also accelerates HIV disease progression, increasing infectivity and reducing HIV treatment efficacy.

“The synergy of TB and HIV has created a worldwide public health crisis and has significantly complicated attempts to eliminate TB in both the industrialized and developing worlds,” noted Rodwell.

Rodwell’s team analyzed San Diego County TB surveillance data from 1993 through 2007, grouping cases by HIV status: positive, negative or unknown. Of the 5,172 TB cases analyzed, 8.8 percent were also infected with HIV. The number of new co-infected cases did not change significantly during this period, but the proportion of cases among Hispanics did increase significantly, while the proportion of cases among non-Hispanic white and black patients decreased.

Hispanics now account for more than 80 percent of all TB–HIV co-infection cases in the county, further widening existing health disparities in this region. Co-infected patients are significantly more likely to be Hispanic 30 to 49 year-old male injection drug users than any other patient group. Researchers recommend that since the burden of TB and HIV in San Diego has shifted to Hispanics, the disparity must be addressed with focused binational TB and HIV prevention efforts.

Rodwell explained, “With more than 40,000 people crossing the border between Mexico and San Diego on a daily basis, and our finding that the majority of new TB–HIV co-infection cases occurred among Hispanics that were born in Mexico, it is clear that future interventions to address this health disparity will need to be binational in nature.”

Published in the January/February 2010 issue of the journal Child Development, the study was conducted by scientists at Leiden University in the Netherlands. One of the researchers, doctoral student Natasha Dobrova-Krol, is of Ukrainian origin.

The researchers sought to examine the effects of HIV infection and being raised in institutions on the development of 58 infected and uninfected Ukrainian 4-year-olds. Some of the children lived in institutions from shortly after birth, while others lived with their biological families.

The study found that the quality of the relationships between the children and their caregivers had a bigger impact on children’s physical growth and cognitive performance than the presence of the HIV infection or the quality of the physical environment. In addition, the study found that for both children with and without HIV, family care, even when it was compromised, was better for children than institutional care.

“This study underscores efforts to strengthen the quality of children’s relationship with caregivers as important for children infected with HIV,” suggests Marinus H. van IJzendoorn, professor of child and family studies at Leiden University, who worked on the study.

“Because HIV-infected children are the least-preferred candidates for adoption or foster care, many of them will remain in rather low-quality institutions. Renovating the premises and giving them toys and learning materials has become a popular form of intervention in Eastern Europe, and it is certainly valuable. But our study shows that interventions should focus on more stable and sensitive relationships between children and their caregivers.”

The researchers suggest that changing the work schedules of part-time workers enhances caregiver stability. They also developed a training program for caregivers and parents, based on feedback of videotaped interactions between adults and children, that was effective in promoting basic parenting skills and, they suggest, should be tried out in orphanages.

The study, conducted by the Partners in Prevention HSV/HIV Transmission Study, was released by the New England Journal of Medicine in its online edition Jan. 20 and will follow in the print edition Feb. 4.

The largest risk group worldwide, but particularly in Africa and Asia, for contracting HIV is stable, heterosexual couples where only one partner is infected. Among those infected, about 90 percent also have a herpes simplex virus-2 (HSV-2), the most common cause of genital herpes, said study co-author Kenneth H. Fife, M.D., Ph.D., professor of medicine in the Division of Infectious Diseases at the Indiana University School of Medicine.

“Logic indicated that outbreaks of HSV-2 sores could enhance the transmission of HIV,” said Dr. Fife. “This is the first comprehensive study to look at the potential for reducing the transmission of HIV through treatment of the herpes virus.”

Multiple studies have shown that frequent genital herpes recurrences increase the amount of HIV in the blood and genital tract. It is known that HIV virus is shed through genital herpes ulcers and people with those ulcers transmit HIV to other more efficiently.

Five preliminary studies showed that it is possible to decrease the amount of HIV in the blood and genital tract through treatment to suppress HSV-2. However, those studies did not measure whether there also was a reduction in HIV transmission.

The study found that acyclovir reduced the occurrence of HSV-2 genital ulcers by 73 percent and thus the amount of HIV present in the blood and genital tract decreased twofold.

In spite of the reduction of HIV present in blood levels, the researchers found there was no significant difference in the transmission of HIV. Laboratory testing showed there were 41 infections in the group taking acyclovir and 43 in the placebo group.

“This new compound, EFdA, is 60,000 times more potent than any other drug that is currently being used to treat HIV,” said Stefan Sarafianos, assistant professor of microbiology and immunology in the MU School of Medicine and investigator in the Christopher Bond Life Sciences Center. “This compound has a different chemical makeup than other approved therapies and creates an exceptional amount of antiviral activity. EFdA is activated very quickly and stays long in the body to fight the virus and protect from infection.”

When a person is exposed to HIV, the virus invades healthy cells that play an important role in keeping the body’s immune system strong. In order to multiply itself and remain in the body, the HIV virus relies on certain proteins. One protein, known as reverse transcriptase, is the main HIV enzyme responsible for viral replication. Effective HIV drugs control the virus by blocking the functions of these viral proteins.

EFdA is a nucleoside reverse transcriptase inhibitor (NRTIs). NRTIs target reverse transcriptase and can stop the virus from duplicating and spreading. Currently, there are eight clinically approved NRTIs, but they can protect cells for only short periods of time. With EFdA, patients could be protected for two days instead of few hours and would not need to take the drug as often, Sarafianos said.

“Infection is the result of an overwhelming attack of the virus, but if you manage to keep the viral load low, the body has a mechanism to defend itself and clean up the virus on its own,” Sarafianos said. “The goal of our research is to drop the virus to very low or “undetectable” levels. Patients with suppressed viral loads will have increased life expectancy. Not all drugs work with all patients, and new resistant viral strains develop. Therefore, it’s important to keep adding to our possible options for therapy.”

Sarafianos hopes EFdA also can double as a preventative agent in the form of a vaginal gel or cream. This would provide additional protection to women whose partners refuse to use condoms.

Sarafianos collaborates with Michael Parniak, at the University of Pittsburgh and Hiroaki Mitsuya at the National Institutes of Health. Sarafianos’ recent research was published in The Journal of Biological Chemistry.

Blood flow in the brains of HIV patients is reduced to levels normally seen in uninfected patients 15 to 20 years older, scientists report online in The Journal of Infectious Diseases.

“The graying of the AIDS patient community makes this infection’s effects on the brain a significant source of concern,” says first author Beau Ances, M.D., Ph.D., assistant professor of neurology at Washington University. “Patients are surviving into their senior years, and a number of them are coming forward to express concerns about problems they’re having with memory and other cognitive functions.”

Epidemiologists estimate that 14 percent to 18 percent of all AIDS patients in the United States are more than 50 years old. This age group also has one of the highest rates of new infection. If current trends continue, by the year 2015, their number will grow to more than 50 percent of the overall patient population.

Prior studies of HIV infection’s long-term health effects have found the virus may adversely affect the heart, liver, endocrine system, skeleton and kidney. A recent study of the overall health of the body found that HIV infection advances the body’s age by about 10 years. HIV can lead to dementia in some patients, but scientifically quantifying the effects of HIV and aging in the brain has been challenging, according to Ances.

“We believe the virus crosses into the brain using infected immune cells,” Ances says. “Once in the brain, HIV doesn’t directly infect neurons but instead affects supporting cells that can release immune factors that harm neurons.”

Researchers including Washington University’s David Clifford have detected similarities between HIV-associated dementia and Alzheimer’s disease (http://news.wustl.edu/news/Pages/15182.aspx). However, adapting the cognitive tests used in diagnosis of Alzheimer’s disease to HIV research has been difficult. Problems have included the time burdens the tests place on patients, socioeconomic factors prevalent in the AIDS patient population that make standardizing test results challenging and the lack of centers that have the capability to perform such tests.

In an attempt to find a quicker alternative available at many hospitals, Ances and his colleagues turned to magnetic resonance imaging scanners and a new technique known as arterial spin labeling that allows precise, non-invasive blood flow measurement.

Ances used this approach to assess brain blood flow in 26 subjects with HIV and 25 uninfected controls. Both groups were comparable in mean age range and education, and researchers screened participants for confounding factors such as head injuries, neuropsychiatric disorders and substance abuse.

When individuals were resting in the scanner, brain blood flow values were significantly reduced in subjects with HIV compared to uninfected controls. These reductions decreased brain blood flow to levels roughly equivalent to readings seen for uninfected individuals 15 to 20 years older.

When scientists asked participants to perform a visual task, which normally triggers an increase in blood flow to particular regions of the brain involved in the task, participants with HIV had greater blood flow increases, suggesting the brain and its support systems had to work harder to get the task done.

Researchers also found that HIV reduced brain blood flow even among young, recently infected patients, reinforcing earlier results that they previously published.

“Brain blood flow levels decline naturally as we age, but HIV, the medications we use to control it or some combination of the two appear to be accelerating this process independent of aging,” Ances says.

Alzheimer’s researchers have long recognized that the disease can do damage to the brain for years before clinical symptoms appear. The brain appears to be able to adapt to ongoing damage up to a threshold, and at that point symptoms become apparent. It is not clear if a similar phenomenon is taking place in HIV patients as they age.

Typically physicians use blood tests that quantify the levels of HIV in a patient’s blood to determine when to start medications. Ances says the new results suggest that the virus’ effects on the brain may be another factor to consider.

“Could we reduce the harmful effects of the virus if we started treatment earlier, or does treatment significantly contribute to the harm that’s being done?,” Ances asks. “These are the kinds of issues we urgently need to start examining as the AIDS patient population ages.”

“We want to crack the code of resistance,” said Wei Wang, associate professor chemistry and biochemistry at UC San Diego who led the collaboration along with Jun Liu of Harvard. The team reports their work in this week’s early online edition of the Proceedings of the National Academy of Sciences.

HIV replicates quickly, but the copies are imprecise. The constant mutation has made HIV infection difficult to treat, much less cure, because drugs designed to interrupt the cycle of infection fail when their targets change.

To better understand which mutations matter for drug resistance, the researchers compared sequences of HIV taken from patients treated with specific drugs to those from untreated patients. Using a novel statistical method, they identified clusters of mutations that seemed to be working together to help the virus escape treatment.

One drug, indinavir, targets a protein called protease, which the virus needs to assemble the capsule it uses to invade new cells. Substitutions in ten different places on protease occurred in patients who were taking the drug, but what combination of mutations would hinder the action of the drug wasn’t clear before this analysis.

Chemists can determine how a drug fits to a particular protein using computer modeling, but those computations take considerable time. Evaluating all possible combinations of those 10 substitutions is impractical. The statistical screen narrowed down the possibilities.

“People never looked at this, because they didn’t know which mutation or which combination of mutations to study,” Wang said. “That’s the advantage of using the statistical method first to find the patterns. After the statisticians discovered the connections between mutations, then we focused on those combinations. We built structural models to understand the molecular basis of drug resistance.”

Using the computing resources of the Center for Theoretical Biological Physics at UC San Diego where Wang is a senior scientist, they worked out how the substitutions would change the shape of protease and its affinity for the drug. One set of changes, for example, would tend to dislodge the drug from the pocket where it normally fits.

The researchers also determined that the mutations must happen in a particular order for replicants to survive treatment with indinavir, a window into how drug resistance develops.

Looking back into the database at samples taken from individual patients at several different times during the course of their treatment, the team found that mutations accumulated in the orders that they predicted would be possible during drug treatment. Sequential mutations that their models predicted would leave the virus vulnerable to drug treatment were not observed.

The team reports its results for two additional drugs, zidovudine and nevirapine, which target a different viral enzyme, in this paper and is extending its work to all nine drugs currently approved by the FDA to treat HIV.

“Our analysis found that greater antiretroviral therapy adherence was associated with lower direct health care costs for HIV-infected adults who received care through a large HIV/AIDS disease management program in South Africa,” said Jean B. Nachega, MD, PhD, MPH, lead author of the study, associate scientist in the Bloomberg School’s Department of International Health, professor of Medicine and director of the Center for Infectious Disease at Stellenbosch University, Cape Town, South Africa. “Cost for hospitalization increased from 29 percent to 51 percent of total costs as antiretroviral therapy adherence decreased, and this increase explains the difference in total mean monthly heath care costs from the lowest to the highest antiretroviral therapy adherence quartile.”

Researchers conducted a cohort study to determine the effect of antiretroviral therapy adherence on direct health care costs among 6,833 HIV-infected adults. Study participants were enrolled in Aid for AIDS, a private-sector HIV/AIDS disease management program in South Africa between 2000 and 2006. Nachega, along with colleagues from the Bloomberg School, University of Cape Town and Aid for AIDS, averaged monthly direct health care costs and categorized pharmacy claim adherence in quartiles, from 1 to 4. Independent effects of patient characteristics on monthly total health care costs were assessed with advanced health econometrics models.

“The cost savings are largely related to less hospital use. The threat is that budgets for hospitals are often divorced from budgets for outpatient AIDS treatment. In fragmented health systems it is difficult for the outpatient administrator to rationalize investments that lower the costs for hospitals. A broader view is necessary to improve patient care and save money,” said David Bishai, MD, PhD, co-author of the study and associate professor in the Bloomberg School’s Department of Population, Family and Reproductive Health.

“Effective, practical intervention strategies to promote, as well as to proactively monitor antiretroviral therapy adherence, are badly needed as they may save direct health care costs by decreasing patient’s morbidity and mortality and are likely to be cost-effective in the long-term,” added Nachega.

“Association of Antiretroviral Therapy Adherence and Health Care Costs” was written by Jean B. Nachega, Rory Leisegang, David Bishai, Hoang Nguyen, Michael Hislop, Susan Cleary, Leon Regensberg and Gary Maartens.

The research was supported in part by grants from The National Institute of Allergy and Infectious Diseases (NIAID), NIAID Mentored Patient-Research Career Award, the John McGoldrick Senior Fellowship Award for Biostatistics in AIDS Research and the Doris Duke Charitable Foundation’s Operations Research in Africa (ORACTA) Program.

And these bacterial changes may also be associated with earlier observations that women whose male partners are circumcised are less likely to develop bacterial vaginosis, an imbalance between good and harmful bacteria.

The study — The Effects of Circumcision on the Penis Microbiome — could lead to new non-surgical HIV preventative strategies for the estimated 70 percent of men worldwide (more than 2 billion) who, because of religious or cultural beliefs, or logistic or financial barriers, are not likely to become circumcised.

“It has important public-health ramifications,” said Dr. Lance B. Price, Director of TGen’s Center for Metagenomics and Human Health and co-lead author of the scientific paper, which describes the world’s first molecular assessment of the bacterial diversity of the male reproductive organ.

This new study is part of a larger effort by the U.S. National Institutes of Health to study and describe the “human microbiome” — the microbes that exist collectively on and in the human body. Other projects are focused on microbiomes involving the skin, nose, mouth, digestive and female genitourinary tract. Jointly, the goal of these projects is to define the various roles of microbes in human health and disease.

In investigating the impact of male circumcision on the penis microbiome, a collaborative team from TGen and the Johns Hopkins Bloomberg School of Public Health found for the first time that circumcision significantly changes the bacterial community of the penis.

Other epidemiological studies have shown that male circumcision is associated with significant reductions in HIV acquisition in men.

The strongest evidence for a cause-and-effect relationship between circumcision and HIV risk reduction came from three randomised-control trials in sub-Saharan Africa, where the circumcision rate is relatively low and the HIV infection rate is relatively high. All three demonstrated a more than 40 percent reduction in HIV acquisition among circumcised men.

The largest of these three studies — in Rakai, Uganda — was led by Dr. Ronald H. Gray, a renowned epidemiologist at Johns Hopkins and the scientific paper’s senior author. Dr. Gray’s group collected penile swabs from all of the circumcision trial study participants, which provided the data for the new TGen-Johns Hopkins study.

The new study found that circumcision — the removal of the foreskin, or prepuce, from the penis — eliminates an area of mucous membrane and dramatically changes the penile bacterial ecosystem. Significantly, TGen’s analysis of more than 40 types of bacteria, using a 16S rRNA gene-based pyrosequencing approach, suggests that the introduction of more oxygen following circumcision decreases the presence of anaerobic (non-oxygen) bacteria and increases the amount of aerobic (oxygen-required) bacteria.

“This study clearly shows that male circumcision markedly reduces genital colonisation with anaerobic bacteria in men,” said Dr. Gray, the William G. Robertson Jr. Professor in Population and Family Planning at the Johns Hopkins Bloomberg School of Public Health.

“These bacteria, which cannot grow in the presence of oxygen, have been implicated in inflammation and a number of infections affecting both men and women. Our randomised trials have shown that male circumcision prevents HIV infection in men and protects their female partners from vaginal infections, especially bacterial vaginosis. It is possible that the virtual elimination of anaerobic bacteria by circumcision contributes to these benefits of the procedure,” Dr. Gray said.

Several mechanisms have been proposed for how circumcision reduces HIV acquisition in men:

• Circumcision reduces the amount of mucosal tissue exposed to vaginal secretions during heterosexual intercourse and thus may reduce the potential interactions between the virus and its target immune cells.
• Circumcision results in a process called keratinization, whereby the top layer of the inner foreskin becomes thicker, which may provide additional protection for the underlying target immune cells.
• Circumcision-associated physiological changes of the penis — including lower moisture and oxygen availability around the head of the penis — may reduce the number of pro-inflammatory anaerobic bacteria that could make the target immune cells more vulnerable to HIV infection.

“These potential explanations are not mutually exclusive and may work in concert to reduce HIV risk,” said Dr. Price, an Associate Investigator in TGen’s Pathogen Genomics Division.

The new study found that specific bacteria taxonomically defined as anaerobic dominated the microbiota of the penile coronal sulcus before circumcision. However, after circumcision, these bacteria decreased dramatically.

“Thus, the reduction in the putative anaerobic bacteria after circumcision may play a role in protection from HIV and other sexually transmitted diseases,” the study concluded.

Bacteria that form in the absence of, or lower levels of, oxygen may be associated with inflammation and the activation of Langerhans cells. These cells, which are part of the body’s normal immune system, work to capture and degrade the virus when they are in an inactivated state. But once activated, the Langerhans cells become re-directed to assisting HIV infection by presenting the virus to CD4+ cells.

Circumcision remains a controversial procedure that has ardent proponents and opponents. Those who favor circumcision point to many studies demonstrating lower risk for sexually transmitted diseases associated with circumcision. Those who oppose circumcision point to the potential dangers of the procedure itself as well as cultural concerns.

This new study shows that circumcision significantly changed the penile bacterial ecology.

“The concept that there are good and harmful bacteria is essential to studying the human microbiome. Our work showed that the profile of the penile bacterial communities changed significantly after circumcision,” said Dr. Cindy M. Liu, a medical doctor and researcher at both TGen and Northern Arizona University. She is the paper’s other co-lead author.

“With the decrease in putative anaerobic bacteria, we saw a correlated increase in the proportion of other specific facultative anaerobic and aerobic bacteria. This suggests that eliminating harmful bacteria may be only half of the needed action. Ensuring that the niche left by pre-circumcision anaerobic bacteria are filled with “good” bacteria will also be critical,” Dr. Liu said.

TGen and Johns Hopkins researchers plan to conduct more studies to determine whether specific bacteria are associated with increased HIV risk and if such bacteria can be eliminated using non-surgical strategies.

“As HIV-infected individuals live longer with potent antiretroviral therapy (ART), metabolic complications such as low bone density and osteoporosis are increasingly recognized,” said Michael Yin, MD of Columbia University Medical Center in New York and lead author of the study. “Although numbers of HIV-infected postmenopausal women are increasing and postmenopausal women are at highest risk for osteoporotic fractures, few studies have evaluated skeletal status in this group. We hypothesized that postmenopausal women might be particularly vulnerable to the adverse effects of HIV infection or ART on the skeleton and our results indicate that this may indeed be the case.”

To test their hypothesis, Yin and his colleagues initiated a longitudinal study to assess bone health in 92 HIV-positive and 95 HIV-negative postmenopausal women. Bone mineral density of the lumbar spine, femoral neck and hip as well as body composition were measured by dual x-ray absorptiometry (DXA). Researchers found that HIV-positive postmenopausal women had lower bone mineral density at both the spine and hip than HIV-negative postmenopausal women.

“HIV infection was independently associated with lower bone mineral density after adjusting for body mass index (BMI) and traditional osteoporosis risk factors,” said Yin. “While the reason for HIV-associated bone loss remains unclear, it may be related to increased levels of cytokines (proteins produced by cells that aid communication between cells), direct effects of antiretrovirals on bone cells or hormonal/nutritional deficiencies that are common in HIV.”

“Estrogen protects against the effect of cytokines on bone resorption,” said Yin. “Therefore, as HIV-positive women become estrogen deficient during menopause, they may be at higher risk for accelerated bone loss and fracture.”