In the Epidemic's Heart

The Centre for the AIDS Programme of Research in South Africa, CAPRISA, has been working to unlock the secrets and weaknesses of HIV and TB for years. With a spate of ongoing and planned trials, researchers hope to soon turn the tables on the deadly diseases.

By Michael Keller

In a waiting room inside Durban, South Africa’s eThekwini research clinic, Dr. Nigel Garrett, wearing a white lab coat and a couple of days of facial stubble, talks with five waiting volunteers. Between Garret and the volunteers is a side table stacked with slices of white bread for noshing as they wait for their names to be called. A television mounted to the pinkish-beige institutional walls buzzes with a daytime show over Garrett’s shoulder.

Nurses and case workers emerge from and enter the door to a small examination and treatment room connected to the waiting area. Inside that room, one woman sits at a table and records numbers on spreadsheets, the anonymized identifications of the people outside and the trial biopharmaceuticals they are about to receive.

The waiting volunteers, all HIV free, are some of the first to receive an experimental prevention approach—passive transfer of broadly neutralizing monoclonal antibodies to prevent transmission of HIV. These volunteers are enrolled in the multinational Phase IIb Antibody-Mediated Prevention (AMP) Study and will receive repeat infusions of a broadly neutralizing antibody (bNAb) known as VRC01 (J. Virol. 85, 8954, 2011). This antibody is one of several that has recently shown early promise in preventing infection in monkeys (Nature 533, 105, 2016). The Centre for the AIDS Programme of Research in South Africa (CAPRISA), a consortium of five institutions in South Africa and the US, started enrolling participants in May at eThekwini clinic and will eventually recruit more than 100 people in this two-year trial. The facility is one of 15 sub-Saharan African sites chosen to be part of the randomized, placebo-controlled study. Volunteers will receive the VRC01 antibody or placebo by intravenous infusion every eight weeks and be monitored to see if they contract HIV.

“How are you doing today?” Garrett asks a woman who is sitting closest to him. She smiles and nods her head amiably. The two make small talk.

Later, to a visitor, he says, “These people are really so generous with their time. For the AMP Study, the first infusion takes an hour and then we monitor them for negative reactions for another 30 minutes, then it takes 30 minutes for every infusion after. We have a party every three months to give people updates about these studies, and they’re generally very positive about them. These participants are making a real contribution.”

Volunteers for trials that CAPRISA runs at eThekwini clinic, which involve testing HIV vaccine candidates and other prevention approaches, as well as possible treatments, enroll either after walking into the clinic or through community recruitment efforts, Garrett says. To recruit participants, teams canvass neighborhoods to identify people willing to take part. Each volunteer is paid up to US$25 per visit, depending on travel time and the onerousness of the procedure. Recruiters don’t stress the compensation, though, because “we don’t want to give people the wrong incentive to take part,” Garrett notes.

Inside the clinic, all is peaceful. Nurses and technicians quietly shuttle patient samples to the on-site laboratory for analysis. Outside the facility’s walls is a different matter. eThekwini clinic is situated in the heart of the city’s transportation hub. Trains and buses arrive at their respective stations throughout the day from the outlying townships. Minibuses and taxis take the people who arrive there to and from work all over Durban. And the whole hub rises up amidst the city’s main outdoor markets, where sellers, in stalls and out on the street, hawk fruits, incense, beads, and music. Charcoal smoke and the smell of cooking meat waft through the air as several old men play a game of pool on a table that has been wheeled onto the sidewalk.

eThekwini adjoins the Prince Cyril Zulu Communicable Disease Center, the largest outpatient tuberculosis (TB) and sexually transmitted infection (STI) treatment facility in Durban. Their location is strategic—some 460,000 commuters and at least 6,000 street vendors come through the area on an average day. The two clinics receive the sick who are city residents or coming into Durban to shop or work from villages in the surrounding KwaZulu-Natal province. Patients start lining up for diagnosis or treatment beginning at five in the morning, and more than 300 can come through the door in a day. Many have TB, and 80 percent of the people presenting with that disease also have HIV.

“Here you see the worst because they’re coming in on their own after symptoms start occurring,” says Garrett, an HIV and sexual health specialist who relocated from the UK because he said he wanted to be at the center of the epidemic. “Most people come in with persistent coughing, weight loss, bringing up sputum. We need to get their TB symptoms under control a bit and then quickly start them on ART [antiretroviral therapy].”

One of CAPRISA’s main research focuses is HIV and TB coinfection. In 2012, 88,000 South Africans living with HIV died of TB. That’s more coinfection deaths than in the next three African countries with the highest coinfection rates combined. The widely cited 2010 CAPRISA 003 TB-HIV treatment study helped optimize the starting time of ART during TB therapy (NEJM 362, 697, 2010). Up to that point, many clinicians had delayed ART because it could negatively interact with TB drugs. But the researchers found that treating both deadly infections at the same time reduced overall patient mortality by 56 percent. This evidence helped accelerate the international adoption of new treatment guidelines. CAPRISA says the combined therapy now saves an estimated 10,000 South African lives a year.

“The problem in South Africa is that we started HIV treatment very late—that’s why we’ve got such a problem here,” says Garrett. “The idea now is to test as many people as possible for HIV, treat as many as possible, and keep the virus suppressed in their system. We treat TB at the same time.”

Just before noon at the eThekwini clinic, business has settled down since the morning and only a dozen people wait in the communicable disease center. Upstairs, up to 6,000 patients are being treated for HIV and TB. Garrett, CAPRISA’s head of vaccine and pathogenesis research, strides through the communicable disease admission area with his disposable respirator covering his mouth and nose, taking it off when he enters the prevention wing. The day is just beginning for his team.

On the frontline

eThekwini is one of three research clinics CAPRISA runs. It also operates the nearby Springfield clinic at Durban’s King Dinuzulu Hospital, which focuses on clinical studies to treat drug-resistant TB, and the Vulindlela clinic outside Durban in rural KwaZulu-Natal province, the epicenter of the decades-long AIDS epidemic. In 2012, the last year for which official data is available, the southeastern province had an HIV prevalence rate among all people age two years and older around 17 percent. If looking at only people 25 years and older, the prevalence in the province shoots up to 30 percent. By comparison, the global rate was around 1 percent. These provincial numbers represent the highest percentage of people living with HIV in South Africa, which itself has the world’s most infected people—around 7 million.

It is these stark realities, along with CAPRISA’s work on understanding the virus and developing prevention and treatment approaches, that have made the organization and its 200 scientists and graduate students a renowned research and educational center on the frontline of the epidemic. The effort is coordinated from an office on the campus of the University of KwaZulu-Natal’s Nelson R. Mandela School of Medicine. The headquarters is a modern work of glass-and-concrete architectural art.

In the waiting area outside CAPRISA’s offices on the second floor stands a working child’s toy—a maze where anyone can pick up a marble from below, drop it in at the top, and watch as it careens down wire pathways like a roller coaster ride. Plastic arms randomly send the marble down different avenues to the bottom—perhaps a fitting analogy for CAPRISA’s scientific pursuits. The organization currently lists 24 trials and studies ongoing or in some stage of approval or data analysis. Promotional materials proudly announce that institute researchers have been authors of more than 350 articles published in peer-reviewed journals, and produce an average of 50 new journal articles a year.

With so much research news to share, it is understandable that Salim Abdool Karim, an infectious diseases epidemiologist who is CAPRISA’s director and cheerleader-in-chief, could rarely be found around the office when the 21st International AIDS Conference (AIDS 2016), the preeminent meeting on the epidemic, came to town in mid-July. During that week, he and wife Quarraisha Abdool Karim, another infectious diseases epidemiologist and CAPRISA’s associate scientific director, were a blur. The power couple remained in motion except when planted on one of the stages inside Durban’s International Conference Center. Between them, they were featured speakers in eight sessions over the conference’s five days. Other center researchers like Garrett spoke at another nine sessions.

On the last day of AIDS 2016, the two finally got a chance to sit down for a quiet working lunch at the center’s headquarters. A couple of days before, Salim’s lunch hour was spent on a stage with Bill Gates in front of thousands of researchers and advocates packed into a dark auditorium. Now Salim and Quarraisha shared quiche and salad while providing a narrative of CAPRISA’s past and future for a couple of visitors. Salim, in a tan suit and light blue, short-sleeved shirt, leaned back into the office chair. His face seems to be permanently open in a warm smile beneath his salt-and-pepper goatee. While Quarraisha comes off as quieter, studious, and more comfortable rattling off deeply complex biomedical research data, Salim appears relaxed and gregarious as he lists the recognitions his team has earned.

He takes special pleasure in informing guests of the overwhelming number of women—82 percent of the staff—working throughout CAPRISA. “We are essentially a women’s organization,” he says. “We have a policy of giving women preference, and it just turns out that we get a lot of women who apply. We don’t have a male statistician or pharmacist in the organization.”

An approach targeted at women

CAPRISA’s focus on women extends beyond its internal staff. The organization is also heavily invested in countering the unequal burden AIDS places on girls and young women. In 2012, more than 14 percent of all South African women had contracted the virus compared to a prevalence rate of under 10 percent of men.

During AIDS 2016, researchers released findings that illuminated a reality in South Africa’s epidemic that at least partially answers why this is so. From population studies, investigators could see that women were getting infected years before males of the same age. CAPRISA scientists analyzed the genetic code of HIV found in 1,589 people living in either rural or urban settings. In their still unpublished study, the team was able to connect new infections in girls and young women to men eight years older than them on average. This characteristic perpetuates a cycle of infection that continues when the newly infected females transmit the virus to males of similar age. “It’s not about having sex at this young age. Sex with peers gets you pregnant and other STIs,” says Salim. “Having sex with older men gets you HIV. Older men allow HIV’s entry into younger women. If you can keep the 15- to 24-year-old group uninfected, you can break the chain of transmission.”

CAPRISA has been developing tools specifically for young women to prevent HIV transmission. A study whose results were released in 2010, the CAPRISA 004 tenofovir gel Phase IIb trial, was the first to show that an antiretroviral-based microbicide could be used to prevent sexual transmission of HIV (Science 329, 1168, 2010). The product, a vaginal gel, was meant for women to take prevention into their own hands, and the initial results excited the scientific community. The team of scientists from CAPRISA, Family Health International, and South Africa’s National Institute of Communicable Diseases found that vaginal administration of a gel containing one percent tenofovir up to 12 hours before sex and as soon as possible within 12 hours afterwards reduced HIV infection in women by 39 percent. It also reduced genital herpes infection by 51 percent. When it was announced during AIDS 2010 in Vienna, the crowd broke out into applause and a standing ovation.

This unabashed optimism was tempered later by a series of studies showing the approach was ineffective. A study published in 2013 called Vaginal and Oral Interventions to Control the Epidemic (VOICE) failed to show tenofovir gel’s efficacy among more than 5,000 women in sub-Saharan Africa. “The data on tenofovir gel and tablets in women has been all over the place,” says Salim. “It’s about adherence. The participants don’t know how to use the products. You have to focus on drug levels—if a woman misses one dose out of seven, her tenofovir levels are wiped out.”

Those who used the gel and had detectable drug levels in blood saw a significantly lower risk of contracting the virus. But subsequent tests of stored blood samples in 2014 found that only 30 percent of participants used the products regularly, and follow-up interviews found widespread inconsistency in use. Undeterred, researchers at CAPRISA and elsewhere are working to produce a PrEP product for women that isn’t as dependent on user adherence. Current candidates include a vaginal ring and an injectable antiretroviral (ARV). The center contributed to one study called ASPIRE, which used a vaginal ring containing the experimental ARV dapivirine. Results published in February showed the ring modestly reduced the rate of infection by 27 percent (NEJM doi: 10.1056/NEJMoa1506110). Another analysis of the ASPIRE data released in July at AIDS 2016 showed that, in those women who used it as directed, the ring reduced the infection rate by 65 percent across all age groups. Meanwhile, CAPRISA is also taking part in another, ongoing Phase III dapivirine ring study called MTN 020.

“We know the more you use a product, the more protection you have,” says Quarraisha. “But even among high adherers, you don’t get complete protection. What else is a factor? We know the amount of ART at the point of infection is important because commensal bacteria in the vagina are depleting the drug. So we have to look beyond adherence to the biology of women.”

These considerations have led CAPRISA’s researchers to investigate how the bacterial microbiome in the vagina may play a role in HIV infection, protection, and drug interaction. In a small, unpublished analysis of the vaginal bacterial community of 119 South African women, scientists recently found that an overgrowth of Prevotella bivia, an opportunistic pathogen, increased the chance of HIV infection 13 times over those with less or none of the bacteria. This may be due to the bacteria’s release of lipopolysaccharide, an immune system stimulant that can increase genital inflammation up to 20 times and therefore make people more susceptible to HIV infection. Prevotella bivia has long been associated with bacterial vaginosis and pelvic inflammatory disease (Clin. Infect. Dis. 20, S271, 1995). Salim and his colleagues published studies last year that showed how the inflammation cascade, including elevated inflammatory cytokines in the female reproductive tract, recruit more HIV-susceptible immune cells to mucosal surfaces (Clin. Infect. Dis. 61, 260, 2015). Once there, they provide a target-rich environment for the invading virus (Mucosal Immunol. 9, 194, 2015).

Another cohort analysis showed how the complexities of the microbiome can impact the efficacy of HIV prevention approaches. A collaboration between the Public Health Agency of Canada, CAPRISA, and the University of Washington investigated cervicovaginal lavage samples from 688 women who took part in the tenofovir gel study and had 50 percent adherence to the gel application schedule as evidenced by monthly returned empty applicators. They found 188 unique bacterial species in the samples. Of these, the gel protected 61 percent of women who had a more typical genital microbiome dominated by bacterial species of the Lactobacillus genus, reported study team member Adam Burgener of the Public Health Agency of Canada during an AIDS 2016 session. But in women whose microbial communities had shifted to become dominated by other non-Lactobacillus species, such as Gardnerella vaginalis, the protective efficacy was only 18 percent, which was not statistically significant. An unpublished follow-up study showed that G. vaginalis can absorb tenofovir, diminishing the drug’s availability at the infection site. “It turns out that a healthy vagina is important for this prophylactic to work,” says Salim. “So how do you make a healthy vagina? Can we supplement with Lactobacillus? And why does somebody’s microbiome look one way versus another?”

This work has opened up new research pathways that could aid in creating more effective prevention approaches. Among a host of possibilities, Salim posits that combining antibiotics or probiotics with antiretrovirals could make PrEP more forgiving in the event a woman misses a dose. Of this new view into microbial interplay, Quarraisha said: “Here we are three decades into the epidemic and we are trying to find preventions in women when we haven’t figured out some of the basics of women’s biology. If the genital tract’s health is playing an important role in infection, it behooves us to understand this better.”

Pushing forward with new insight and greater hope

Walking through CAPRISA’s clinic downtown and its headquarters gives a small view into how the organization and its research partners work. Within its headquarters, there is a lab that analyzes samples from a network of nine laboratories all over the country. The overflowing space is crammed with sequencers, refrigerators, shelves of reports, walls of cell-sorting machines, and microscopes of both the optical and electron type. One room is dedicated to performing cytokine analysis, another just for DNA preparation.

Taped to a hood, an illustrated procedure checklist shows the proper dissection and manipulation of cervical tissue. Salim notices a visitor reading it and comes over to offer some context. “We grow human vaginas here,” he says proudly. “We get tissue from surgical theaters. We put HIV on them. We put drugs on them. It’s all done here. We have equipment that would be the envy of any university.”

Outside the laboratory’s doors hang pictures of marching protestors taken during the Apartheid era. In one, the camera is focused on a young Salim, who fought against the system since his boyhood in Durban and through his days in medical school until it finally collapsed. That long battle is a fitting lesson about perseverance for the young scientists who pass the picture every day, and then hunker down at their desks trying to find an exploitable chink in HIV’s armor.

Taking several turns after the picture, the space opens up into a bullpen where graduate student researchers sit when not out at field sites working on their projects. Nearby, in an adjacent room cluttered with keyboards and denuded computer towers, information technology specialists are managing the raw information from previous and current trials that is growing every day. Back in the bullpen, giant blown-up front pages from international newspapers like The New York Times that trumpet the center’s studies adorn the walls. They are likely meant to serve as inspiration to the young researchers. One from the Times’s Celia Dugger in 2010 heralded the results of the tenofovir gel trial as a promising tool that could empower women to keep themselves from getting infected.

A search for the ultimate

But to the Karims and the rest of the CAPRISA staff, any means of prevention that requires daily, monthly, or sexual-activity-based maintenance to impart protection from infection is not the ultimate breakthrough against the epidemic they’re hoping to find. Of course, it is well understood that there will be no silver bullet against the virus, and multiple behavioral and pharmacological tools will need to be used together. Still, the most tantalizing aspect of their work, says Quarraisha and Salim, is the possibility of developing an effective and long-lasting vaccine to impart immunity against HIV.

To this end, CAPRISA has become a study site and research partner for several vaccine candidates. During AIDS 2016, the partnership running HVTN 100, a Phase I/II safety and immune system-response trial of the ALVAC/gp120 prime-boost vaccine candidate, released preliminary safety and immunogenicity data from the approximately 250 South African participants, of which 44 were given the experimental vaccine candidates at the eThekwini clinic. These candidates are similar to those tested in the RV144 trial in Thailand, which showed the combination was 31 percent effective at preventing HIV infection. The HVTN 100 vaccine candidates, however, were formulated based on HIV clade C, the more common strain across Africa. The new formulation also includes a different adjuvant known as MF59. Based on the results of this trial, officials green-lighted the large-scale follow-on Phase III efficacy trial HVTN 702, which will begin enrollment soon. CAPRISA intends to enroll 400 of HVTN 702’s 5,400 total participants.

“People wonder how South Africa has made such an investment in finding a vaccine. It all started when we set up CAPRISA in 2001,” says Quarraisha. “This consortium let us follow cohorts before, during, and after infection. We could look at the immune response and at what was going on with the virus at the same time.”

Salim is particularly excited about the burgeoning field of research into bNAbs, the class of immune system proteins that can target and destroy a wide range of HIV strains around the world and are being investigated as crucial components for a new crop of vaccine candidates. One multiyear study, called CAPRISA 002, continues to provide insights into HIV’s progression into AIDS. Among other findings, the 002 research team uncovered the progression of HIV, group M, subtype C infection, which is common in Africa and India. Researchers also identified patients who naturally made bNAbs (Nat. Med. 18, 1688, 2012). Investigation into how the immune system started producing these potent antibodies found they were triggered because a sugar molecule on the virus’s surface switched positions, opening up a window for a bNAb to reach the virus particles and neutralize them.

CAPRISA researchers isolated a family of bNAbs called CAP256 from a local schoolteacher who was a volunteer in the 002 study (J. Virol. 87, 4882, 2013). She was HIV free for several years over the course of the study period and then became infected. The team followed the infection’s progression and her body’s response to it on an almost weekly basis. As the immune response evolved, they noticed she was making antibodies that targeted similar epitopes on the virus as in the RV144 trial (Immunity 38, 176, 2013). One study found that one of these antibodies, CAP256-VRC26.25, neutralized 70 percent of clade C isolates and 57 percent of various clade isolates (J. Virol. 90, 76, 2016). Salim said the promising bNAb should go into trials next year.

Right now, Salim says their work suggests a bNAb-based vaccine of this type would need to be given to a person every four months. But since the average time that girls and young women are vulnerable to infection is around eight to 10 years, he says that would translate to a total of no more than around 40 doses. “If we can protect these girls, then we can break the cycle of transmission,” he says. That is what Salim, Quarraisha, and the CAPRISA network are focused on for now.

“I have never been as optimistic about our prospects of developing a safe and effective vaccine than I am today,” says Salim. “Now that I see what we can do with these broadly neutralizing antibodies, I am full of hope.”

Michael Keller reports from the frontiers of science, technology, and international affairs. His writing has appeared online and in newspapers, magazines, and books, including the graphic novel Charles Darwin’s On the Origin of Species.