CAPE TOWN, South Africa — Jacqualine Ncube is doing everything she can to be among the 40 percent of South African women who remain HIV-negative into middle age.

At 19, she’s already participated in an HIV vaccine trial. She comes to the Desmond Tutu HIV Foundation Youth Centre here in Cape Town every two months to be tested for HIV. She even takes a combination antiretroviral pill every night at 9 p.m. that prevents her from acquiring HIV if she’s exposed. And when it comes to sex, she insists that her boyfriend use a condom. No method is 100 percent protective, she said, so she covers all her bases.

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When asked if her boyfriend ever scoffs at condoms, Ncube cracked a wry smile and shook her head emphatically.

“He’d never tell me something like that, because he knows what the answer is that he’s going to get,” she said. “I’m so rude when it comes to someone telling me what to do. I don’t want to be told what to do. I want to be my own person.”

By some estimates, about 40 percent of HIV infections are associated with biological mechanisms — mechanisms that scientists are just beginning to unravel.

She also wants, she said, “to be protected, always.”

But for a young woman to be protected always in this part of sub-Saharan Africa is a tall order. In some parts of the country, women her age have an 80 percent chance of acquiring HIV in their lifetimes. Not only are the social and economic odds against her, but a fluke of biology may be against her, too. By some estimates, about 40 percent of HIV infections are associated with biological mechanisms — mechanisms that scientists are just beginning to unravel.

Some of that unraveling is being done in real time. At the International AIDS Conference in Durban today, researchers at the Center for the AIDS Programme of Research in South Africa (CAPRISA) will unveil startling new evidence of a bacterial culprit that could be responsible for as many as two out of every five new cases of HIV among women. They’ll also reveal how another bacteria blocks the effectiveness of those pills Ncube takes.

At the heart of these discoveries is an area of research that was once considered a biological dead zone: the vaginal microbiome. Scientists have known since the 19th century that the vagina is colonized by bacteria. But it wasn’t until the 1990s that researchers began to discover the lush diversity of life there — and how that diversity may contribute to women’s risk for HIV. It’s no coincidence, it turns out, that women who live in areas with high rates of HIV also have disproportionately high rates of a microbiome imbalance called bacterial vaginosis (BV). The inflammation caused by BV, and the specific bacteria that make up that imbalance, can increase women’s susceptibility to the virus. With the research presented today, the field — and women’s chances of staying HIV-negative — could take another leap forward.

A Natural, Robust Defense

When Dr. Richard Cone, professor of biophysics at Johns Hopkins University, working on his PhD in the 1950s and 60s, the general attitude toward the vagina was, well, disinterested. In 1882, Albert Döderlein had identified Lactobacillus in the vagina, a friendly microbe that is also present in things like yogurt. And that, Cone said, was that.

“All the work we’ve done in the last 20 years could have been done 100 years ago,” Cone said. “But there was just no interest.”

By the late 1980s and early 1990s, Cone was interested, though. And so were microbiologists like Sharon Hillier, who began her career working in reproductive health, as well as other microbiologists around the world who began to see this as a fertile field of study. Cone, Hillier, and others began submitting grant applications to the National Institutes of Health (NIH). Then, in the 1990s, a leadership change at the agency expanded funding.

Quickly, it became clear that there’s more to the vaginal microbiome than Lactobacillus. Indeed, there’s a world in there. A 2005 study in the New England Journal of Medicine identified more than 100 different types of bacteria in the vagina.

What researchers began to realize was that several strains of Lactobacillus had the power to protect women from sexually transmitted infections (STIs), including HIV — and that others left women even more exposed.

First, the good news. The microbiome has a secret weapon against HIV: lactic acid. But the conditions have to be just right.

Here’s how it works. First, Lactobacillus has to dominate the vaginal microbiome. Second, the pH in the vagina has to drop below 4 — a low pH that conforms, perhaps not coincidentally, with a healthy pH in the gut (stomach pH tends to hover around 3.5). That’s the pH of a dill pickle.

If you have a Lactobacilli-dominated microbiome, you’ve already created a hostile environment for invading bacteria, viruses and even sperm, all of which thrive at a higher pH. But when you combine Lactobacilli-produced lactic acid with a very low pH, the environment isn’t just hostile. The lactic acid becomes deadly to invading bugs, Cone said.

At a very low pH, lactic acid turns into, in Cone’s words, “a small oily molecule” capable of slipping through the membranes of invading cells and releasing acid directly into the bug.

Boom — dead virus.

“The point at which Lacobacillus begins to secrete enough lactic acid to load up the mucosa with protons is at about 3.8,” said Cone. “It gets charged and forms a layer that is truly protective.”

And though the protective effect is modest, it still adds a layer between women and bugs.

“I like to say,” Cone said with a laugh, “that women need protection from sperm and germs.”

Living in Ncube’s World

The problem is that Lactobacillus doesn’t dominate the microbiomes of many of the world’s women — especially women most at risk for HIV. A 2010 study of American women in the Proceedings of the National Academy of Sciences found that Lactobacillus dominated the microbiomes of Asian and white women, but accounted for only 59.6 and 61.9 percent of the microbiomes of Latina and Black women, respectively. The same has been found in sub-Saharan Africa.

That diversity in the microbiome, and the associated higher pH and increased inflammation is part of what we call BV.

Saying someone has BV is as specific as saying that someone has a cold. Yes, BV is associated with specific symptoms, such as watery discharge and malodor. But only specific combinations of bacteria are associated with those symptoms. So it’s possible to have asymptomatic BV — that is, diversity in the microbiome that increases pH but doesn’t cause discharge or odor. And it’s possible to have those symptoms and be so used to them that they don’t strike you as abnormal, or cause you to visit a doctor for treatment.

“Women don’t come in,” said David Fredricks, member of the Vaccine and Infectious Disease Division of the Fred Hutchinson Cancer Research Center and author of that 2005 NEJM article, “and say, ‘My pH is off.’ They say, ‘I have malodor’ or ‘I have discharge.’”

But that’s exactly what’s happening, especially in women at high risk for HIV. In the U.S., the overall BV rate hovers around 29 percent. But for African American women, whose rates of HIV are 20 times higher than their white counterparts, BV rates can be as high as 51 percent. In Ncube’s Cape Town, where four in 10 new HIV infections occur among women 15 to 24, rates of BV reach 47 percent. And more than two-thirds of those women report no symptoms, said Shaun Barnabas, a PhD candidate studying the vaginal microbiome in Cape Town.

Finding the Smoking Gun

And it turns out that none of the bacteria associated with the symptoms of BV are the ones associated with HIV risk. For that, you have to turn to one strain: Prevotella bivia.

At least that’s the finding of a study released today at the International AIDS Conference. The study, based on the sequencing and analysis of the microbiomes of 120 South African women, found that it was only women with P. bivia in their microbiome who also were statistically more likely to have HIV, too—by a lot.

“What we found,” said CAPRISA’s Karim, “was that if a woman had ever had Prevotella, she had an almost 20-fold higher risk for inflammation and HIV acquisition than other women.”

Of the 120 women studied, 10 percent had ever had Prevotella. But that 10 percent accounted for 41 percent of all infections. That means that two out of five women in the study had acquired HIV because P. bivia set the stage.

It does that, Karim said, by producing proteins known to marshal a strong immune response. That signal causes immune cells called CD4 T cells to flood to the vaginal surface. Unfortunately, those cells are exactly the ones HIV targets to infiltrate and co-opt. Unrecognized by the rest of the immune system, those infected cells are transported to the lymph nodes. And voila — swift, efficient HIV infection.

That means that two out of five women in the study had acquired HIV because P. bivia set the stage.

And while the results are based on a small sample of patients and need to be replicated in other parts of the continent and world, the findings are already drawing praise from high places. Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Disease at the NIH, called it “quite an important observation.”

“Being able to identify a specific villain is good,” he said. “Will manipulating the microbiome be the major thing that ends AIDS? No. But is it one of many, many things that need to be pursued, to help us possibly understand the novel ways we can prevent HIV in women? Absolutely.”

HIV Prevention At Stake

But that’s not all Karim’s team discovered. They also unveiled data today that linked another bacterial strain — Gardnerella vaginalis — to lower effectiveness of the HIV prevention pill Truvada in women.

Karim’s team started the study because they had noticed, in HIV prevention trials, that the efficacy rates were all over the place in women. A recent study out of University of North Carolina that predicted that, for women to receive full protection from the HIV prevention pill Truvada, they couldn’t miss even one dose. Gay men, meanwhile, had been shown in other studies to benefit from the full power of Truvada with just four doses a week.

“We need to figure this out,” Karim said he thought.

So they pulled the frozen microbiome samples from women who’d participated in CAPRISA’s study of an HIV prevention gel made from one of Truvada’s components, tenofovir, and started sequencing the microbiome. Pretty soon, a clear picture emerged. Women with Lactobacillus-dominated microbiomes showed “quite a reasonable effectiveness from tenofovir,” he said. “But in women without Lactobacillus-dominated microbiomes, tenofovir had almost no benefit.”

“Gardnerella was just gobbling up the tenofovir. It was taking it inside the cell, so it wasn’t available to protect against HIV.”

So what gives? To find out, they took cultures of Lactobacillus and the other bacterial strains prevalent in the women’s microbiomes and they exposed them to tenofovir. With Lactobacillus? There was almost no effect. The Lactobacillus just sat there, and so did the tenofovir. They coexisted happily. With Gardnerella? Within four hours, half of the tenofovir disappeared. Within 24 hours, almost all of it was gone.

“I was just floored,” said Karim. “Gardnerella was just gobbling up the tenofovir. It was taking it inside the cell, so it wasn’t available to protect against HIV.”

Whether this finding genuinely answers the question of why women have to be so perfectly adherent to Truvada to achieve the same protection as gay men will require further study. CAPRISA’s results were based on tests done in a lab—the real proof will come when researchers treat for Gardnerella and watch how that changes the effectiveness of Truvada in women. Just such a study, on periodic treatment of BV and its affect on other STIs, is underway in Kenya.

Jared Baeten, vice chair of global health at the University of Washington and one of the investigators of the PARTNERS PrEP prevention trial and demonstration project, said that their studies have shown that Truvada has virtually eliminated HIV acquisition in women in their studies. So Gardnerella may not impact the protection women get from oral PrEP.

“I think the results will probably be most relevant to local application of tenofovir in gel form,” he said. “[CAPRISA’s] results are very important for thinking about which medicines to use as microbicides”–that is, topical prevention medicines, like the tenofovir gel.

Still, the results could change how policy makers scale up HIV prevention. In the middle of explaining these results last week, Karim interrupted the conversation to take a call from Dr. Margaret Chan, director-general at the World Health Organization.

A Healthier Future

The good news is that diagnosing and treating BV is simple and inexpensive, even without diagnosing and treating specific strains. You can buy a pH testing kit at a pharmacy and, if the pH is above 4.5, Karim said, you can get a prescription for metronidazole (Flagyl) and treat it yourself. Getting Lactobacillus into one’s microbiome is a little trickier, though researchers are trying to devise a variety of solutions to that problem now.

All this may mean, for Ncube and other women like her, that there’s another tool they can use to keep themselves safe, forever, from HIV. When she spoke to PBS NewsHour, Ncube didn’t know about Karim’s results, and it was unclear if she’d ever been tested or treated for BV. For now, Ncube will keep doing what she can do to protect herself. And when she looks ahead, she said cheerfully, she will keep going, keep protecting herself. She’s willing, for instance, to keep taking the pills as long as it takes for the epidemic to change.

“Forever,” she said, “Yeah, I’m willing to take it as long as it [HIV] lasts.”