A Rise in Resistance

Half the world's people living with HIV are now on treatment. This is a tremendous accomplishment, but a rise in drug resistance is of increasing concern.

By Michael Dumiak

During his stops in dusty clinics in the KwaZulu-Natal hinterland and in inner city Durban, South Africa, the infectious disease physician Richard Lessells is used to seeing the difficulties that come with administering and maintaining an effective HIV treatment response. When the virus shows resistance to the drug regimens, Lessells says it becomes really complicated.

“In the clinics, I see that we are really struggling with maintaining quality of care,” he says. “It’s a very overstretched system.”

He and his colleagues at the South African Treatment and Resistance Network are no strangers to this issue. They wrote the book on it, in fact. The network’s HIV & TB Drug Resistance & Clinical Management Case Book that describes the challenges that clinicians face in managing complex forms of drug-resistant HIV is due to go into a second printing next year. Lessells is working on the new edition over the holidays. In the meantime, he keeps one of the last boxes of the original 2013 printing in the trunk of his car for distribution to health workers in the field. The cases addressed in the book describe how to manage patients when drug resistance occurs, and also how to prevent resistance with better treatment and care.

This summer the World Health Organization (WHO) put its heft and might behind addressing the growing problem of HIV drug resistance, which has frontline medical staff, policy strategists, and funders alike increasingly concerned. Last month, the WHO convened a brief meeting in Johannesburg to review surveillance and progress on the resistance issue. It was following up directly on the heels of a workshop dedicated to HIV drug resistance that was held in Africa for the first time in its 20-plus years.

Precisely how widespread HIV drug resistance is and how much of a problem it will become is difficult to gauge. One certain thing is that it will greatly shape the overall response to the HIV epidemic. It can impact everything from how doctors prescribe therapies and treat patients, to how drugs are priced, as well as the drive and momentum for developing an HIV vaccine or other preventive strategies.

All this while there are still millions of people in need waiting to start treatment in the first place. “Half of the world’s population living with HIV, 19 million, are on therapy, and this is an extraordinary achievement. But we still have more than 17 million who have never started therapy, and a substantial proportion of the 19 million who have defaulted at one point or another and who need to be reinitiated to therapy if they are going to benefit,” says Chris Beyrer, a Johns Hopkins University epidemiologist and former president of the International AIDS Society. “These [people] are in low-income countries where HIV is highly prevalent and who have had challenges with managing antiretroviral regimens in the past, or where in some cases they’ve had issues with stock-outs,” he says, referring to empty shelves in a pharmacy—supply-chain issues which can result in irregular adherence.

“It’s kind of a watershed time,” says Stanford’s Bob Shafer, an infectious disease researcher who has extensively catalogued HIV drug resistance. “Resistance has been going up.” Things may improve mightily in the next five years due to the introduction of the antiretroviral drug dolutegravir, an integrase inhibitor manufactured by GlaxoSmithKline, but Shafer says it is too complex a problem to say the solution lies simply with new and better drugs.

Why resistance develops  

Mutations are one of Darwin’s great engines and the reason why HIV develops resistance to the drugs used to keep it under control. The virus replicates at an extraordinary rate: in early infection, an HIV virus can double its population every 12-16 hours. The copies are not perfect, though. While it is replicating, the virus makes genetic errors of all kinds. While these mutations are chance mutations—there is no conscious intent on the part of a virus, as much as it might seem like there is—the ones that prove beneficial to the survival of the virus are selected for. Among the keepers are those that allow the virus to escape pressure from antiretroviral (ARV) treatment.

The problem of resistance to HIV, then, is as old as the response to the epidemic. It is, after all, what propelled researchers and clinicians toward developing and prescribing the ARV cocktails that turned the tide against the HIV epidemic in the mid 1990s in the US and Europe. When AZT, the first ARV, was introduced as a stand-alone therapy, the virus rapidly developed resistance to it. The viral loads, or the levels of virus in HIV-infected individuals, rebounded after being initially suppressed by the drug. The effort to overcome this AZT-resistant virus led researchers to develop drug combinations. It was a critical moment in the response to HIV when researchers first showed that an ARV cocktail made it much harder for the virus to mutate around the drugs, allowing viral loads of treated individuals to remain suppressed for longer periods of time.

Regimens were then improved and optimized over the years. “Drug resistance was always around the corner,” says Bob Shafer, an infectious disease specialist at Stanford University who helps maintain the publicly accessible HIV Drug Resistance Database that collects data on how often mutations occur with and without therapy. “There were patients who developed viruses with resistance to every drug that was marketed and available.” As new-generation drugs came along, however, resistance receded. It happened because these drugs have a higher genetic barrier to resistance: that is, the virus needs to contain a higher number of mutations to change enough to avoid the drug. Sometimes these mutations make the virus itself unstable.

There are now eight classes of HIV drugs: nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors, fusion inhibitors, entry inhibitors, integrase inhibitors (of which dolutegravir is most prominent), pharmacokinetic enhancers, and combinations of these in a single pill (see image below, The HIV Life Cycle). Because of the quantity of ARVs now available and the variety of regimens that can be created, therapy failure has become much less common overall. In the US and Europe, even though transmission of HIV with drug-resistant mutations may still be common, most of those mutations are to the NNRTIs being superseded by the newer fixed-dosed combinations of drugs.

Mutations in the virus occur at the nucleotide level, which then results in a change in the amino acids that make up the viral protein, thereby changing its shape. Three nucleotides encode each amino acid. Most mutations in HIV are the result of a single nucleotide change, however, some are the results of multiple changes. In most cases an amino acid change leads to reduced binding or less stable binding between the drug and its target. If the resistance is to a protease inhibitor, the mutations are in protease. If it is to an integrase inhibitor, then integrase. Many small interactions are what leads to the connection between a drug and its target protein on the virus, and if even a few are disrupted, the binding between the two is not as effective.

Characterizing these mutations leads to names such as M184V, which affects tenofovir and zidovudine. The mutations are written in a coded nomenclature, with the capital letters signifying the amino acids—M for Methionine, and V for Valine, for example—and the number signifying the position of the amino acid that is changed. M184V is a single-amino acid substitution from wildtype Methionine (M) to Valine (V) at the point 184 amino acid of reverse transcriptase.

At this point, Shafer says, most of the common mutations have been painstakingly characterized and catalogued. A decade ago Shafer’s team and a set of other labs were asked by the World Health Organization to compile a comprehensive list of drug resistance mutations to help facilitate surveillance. The full list ran to 93 mutations. Shafer does not expect to see many more now, having characterized the most common, but he does think the list should be updated to add a few integrase mutations, especially as integrase inhibitors are among the newest classes of drugs, with less known about resistance to them even as they are expanding in use. The assay company Monogram Biosciences also maintains an extensive database of about 150,000 correlations between HIV genotype and in vitro susceptibility to different ARVs. —MD


Newer and better drugs are, however, poised to make a difference. A deal to introduce dolutegravir, an antiretroviral (ARV) that inhibits HIV’s integration into host cells, at affordable prices is due to come into effect soon in lower- and middle-income countries. The Bill & Melinda Gates Foundation and the Clinton Health Access Initiative reached ceiling price agreements earlier this year with India-based generic drug manufacturers Mylan Laboratories and Aurobindo to offer dolutegravir, licensed from developer ViiV, at an average price of US$75 a year per patient. Dolutegravir has been on the market for three years and is already used in fixed-dose combination therapies in wealthier nations under the brand name Tivicay.

Dolutegravir is set to debut in South Africa on a large scale by the middle of 2018. “That will be a game-changer,” Beyrer says. But getting it out to clinics in South Africa, and in the 90-plus other countries the deal covers, is going to be no simple task. Lessells says it became apparent at the Johannesburg workshops that there are differing opinions on how dolutegravir should be rolled out; from some who favor a slow and methodical approach, to those in Botswana, for instance, who want to set a fast pace in uptake.

These questions are all important, sources say, because resistance is both an immediate public health care problem and a potential long-term threat. But there is no way to skirt the issue entirely. “Some levels of resistance are an inevitable phenomenon. As we scale up antiretroviral therapy, we will see some level of resistance as a consequence of the presence of the drugs. As drugs become more widely available, more resistance will be seen,” says the WHO’s Silvia Bertagnolio, a medical doctor and expert on HIV drug resistance. Researchers have kept tabs on HIV drug resistance for years. But between 2012 and 2017, Bertagnolio says, resistance levels to the most common frontline therapies in lower- and middle-income countries under surveillance started climbing over five percent. “Something happened.”

A new regression and meta-regression analysis commissioned by the WHO from the University of London’s Ravi Gupta and his colleagues sets HIV Lifecycle AIDSinfopretreatment drug resistance levels to non-nucleoside reverse transcriptase inhibitors (NNRTIs), the ARV class contained in the most common frontline regimens in lower- and middle-income countries, at 11 percent in southern Africa, 10.1 percent in eastern Africa, 7.2 percent in western and central Africa, and 9.4 percent in Latin America and the Caribbean. These figures are on the increase. The odds in certain populations for developing ARV-resistant virus are rising 23 percent a year in southern Africa, 17 percent in eastern Africa, 17 percent in western and central Africa, and 11 percent in both Asia and Latin America.

In recent years, 14 countries, including Cameroon, Namibia, South Africa, Zimbabwe, and Uganda, have conducted national surveillance of HIV drug resistance following statistical survey methods recommended by the WHO. Based on a systematic review of studies covering 56,000 patients in low- and middle-income countries, the prevalence of resistance to the kind of ARVs most used in these countries—the NNRTIs such as efavirenz and nevirapine whose availability and affordability transformed the nature of HIV treatment—is currently increasing on an annual basis from 11 percent to 29 percent in frontline countries.

“These numbers are worrisome, and they reflect a real problem for real people,” Beyrer says. He and colleague Anton Pozniak recently penned a commentary arguing that the emergence of HIV drug resistance is a very real threat to the astounding gains made in getting people with HIV onto treatment, a signature achievement during the 30-year history of the epidemic (N.Engl. J. Med. 377, 1605, 2017).

Alarming estimates

There are seven million people in South Africa infected with HIV, about 56 percent of whom are on ARV therapy. The most common first-line regimen for treatment in the region, as in most developing countries, consists of the NNRTIs efavirenz and nevirapine. Surveillance data cited by the WHO, as well as those tracked locally, show rates of resistance in the country climbing, says Gillian Hunt, a senior researcher at the South African National Institute for Communicable Diseases’ Centre for HIV and STIs. “The levels of resistance are really quite startling.”

Analysis of HIV drug resistance data led the WHO, the Global Fund to Fight AIDS, Tuberculosis and Malaria, and the US Centers for Disease Control to distribute an action plan last summer in Paris coinciding with the International AIDS Society’s annual meeting. The plan examines HIV drug resistance in what it breaks down into three types: acquired, transmitted, and pretreatment drug resistance. Acquired resistance is when the mutations develop within individuals on treatment. Transmitted resistance occurs when previously uninfected people are infected with an already drug-resistant virus. Pretreatment HIV drug resistance is used as something of a catch-all: it can be either transmitted, acquired, or both, and is detected in people who have never taken antiretrovirals and are just starting on them, or those who are restarting a first-line antiretroviral regimen after an interruption. This set includes, for example, pregnant women who have taken antiretrovirals to prevent transmission of HIV to their children, or people who are using antiretrovirals for pre-exposure prophylaxis (PrEP).

The action plan strongly emphasizes the figures for pretreatment HIV drug resistance. If these figures reach 10 percent or higher within a county’s population, the WHO now urgently recommends shying away from using NNRTIs in frontline regimens and substituting alternatives.

The plan highlights other figures, too: of 11 countries reporting pretreatment drug resistance data, six of them showed levels of 10 percent resistance or more to NNRTI regimens. Prevalence of acquired resistance to NNRTIs range from 4.3 percent to 16.7 percent in individuals on treatment for between one and two years, and from 4.2 percent to 28.3 percent for those on treatment longer than that. It is much higher for those on treatment with unsuppressed viral loads, with figures ranging from 47.3 percent in Zambia to 76 percent in Guatemala. For those with unsuppressed viral loads despite treatment for longer than three years, the prevalence of NNRTI resistance was above 80 percent.

“The human cost of HIV drug resistance cannot be underestimated,” the report warns. People with NNRTI resistance are less likely to achieve viral suppression, more likely to experience virological failure or to die, more likely to discontinue treatment, and more likely to acquire new drug resistance mutations.

Lessells and his colleagues are seeing this and putting it straight into the next edition of their casebook. “It’s more about second-line failure and complex third-line issues and the kind of things we’re seeing more of here,” he says, referring to the iterative failures of HIV drug regimens that can occur in individuals on therapy. Lessells expects issues even with the arrival of dolutegravir. People on therapy stop treatment often, and then return to try new drugs. If they are advised against it, they may go to a different clinic.

“We tell people, OK, you are going to be able to have a fairly normal quality of life and expectancy. But it will be a daily oral regimen for life,” says Beyrer. “That is a big ask.” Yet gaps in adherence to the daily drugs, for whatever reason, can allow the virus to more easily accrue the mutations that lessen the effect of therapy.

People living with HIV in wealthier countries of the world are routinely monitored and tested for drug resistance. But routine testing is expensive—it involves reading viral DNA contained in a blood sample and checking it against the list of drug mutations. Currently the South African HIV Clinicians Society recommends a test, not when a patient is first diagnosed, but when there is evidence that the first-line antiretroviral therapy regimen is failing. Even at that point the test is expensive for South Africa, at about $350, which puts a burden on the health system. “With failure rates, we’re sitting at between 10 and 15 percent on an annual basis. That’s 300,000 genotypes a year. It’s just not doable,” says Hunt. “We’d love to be able to test everybody, but it’s not practically possible.”

Limited testing means resistance may not be detected quickly. “There are cases where people are resistant to NNRTIs and they are not being picked up. And time is going by,” says Beyrer. “There can be 12 months, 18 months, when you are taking drugs and it is not doing you any good, it is not affecting the virus, and mutations are ongoing.”

This is an issue even where health care systems are relatively stable and consistent. It is even more problematic where securing second or even third-line regimens is a challenge. “This is a developing world issue,” Hunt says, which is one reason she was quite pleased that the International Workshop on HIV Drug Resistance and Treatment, for the first time in its 26 years, was hosted in November in Johannesburg. Lessells was there, too, as he, Tulio de Olivera, and their colleagues work on distributing their case book to clinical health workers. Together with South Africa’s Technology Innovation Agency, they have also set up the KwaZulu-Natal Research and Innovation Sequencing Program (KRISP) to try to offer bioinformatics and genomics expertise, including sequencing and diagnostics, and to help build testing capabilities. There are also new testing kits and shotgun sequencing web-based applications that may well bring down costs of monitoring resistance in developing country populations.

Prepping for resistance  

“Our newest and most effective prevention tool, PrEP with daily oral tenofovir-emtricitabine, is also at risk from HIV drug resistance.” With this line in a recent commentary, Chris Beyrer from Johns Hopkins University stirred a lot of feedback and protest (N.Engl. J. Med. 377, 1605, 2017).

Oral pre-exposure prophylaxis (PrEP), the use of antiretrovirals to prevent HIV infection, is slowly making its way into communities as a highly effective HIV prevention option. As it does, there have been a few cases of HIV infection occurring while an individual is on PrEP. If that happens often enough, it could be another way people develop drug-resistant virus. But for now, researchers such as Gillian Hunt from the South African National Institute for Communicable Diseases’ Centre for HIV and STIs, does not see this as a big concern, even though PrEP is licensed in South Africa.“There aren’t huge numbers of people on PrEP,” she says, and the resistance profile is overall very good. “[But] one also doesn’t want to ignore it.”

Beyrer also says that while resistance developing as a result of PrEP use is a concern, it is not on the same level as his much greater concern about resistance to the non-nucleoside reverse transcriptase inhibitors that are the backbone of treatment in many developing countries. —MD


Three years ago the Joint United Nations Programme on HIV/AIDS (UNAIDS) set a target of 2030 for ending AIDS as a threat to public health, framing the target squarely within the United Nations’ development agenda. A big part of the push comes from striving toward “90-90-90” goals: diagnosing 90 percent of all people with HIV, providing treatment to 90 percent of those diagnosed, and ensuring 90 percent of people on treatment achieve virological suppression by 2020 and maintaining those levels into the future. According to the WHO/Global Fund/Centers for Disease Control plan, if NNRTIs continue to be included in first-line antiretroviral therapy regimens, and the level of pretreatment drug resistance to NNRTIs reaches above 10 percent overall in sub-Saharan Africa, that global target to end AIDS by 2030 will be missed.

Beyrer points out that, whether it is because of resistance or, more likely, a combination of many factors, a place like Malawi is getting close to reaching its 90-90-90 goals, yet is not seeing the epidemic diminish in terms of the number of new infections as quickly as expected. Anthony Fauci, director of the US National Institute of Allergy and Infectious Diseases, penned a commentary at the end of October tracing the different steps to meeting the 90-90-90 goals and ending the epidemic. He argues that with enough progress in prevention and treatment—using highly effective contemporary treatments and getting people at high risk of HIV infection to use PrEP—it is, theoretically, possible to get there (J. Amer. Med. Assoc. 318, 1535, 2017). “Ending the HIV/AIDS pandemic without a vaccine is possible,” he wrote, “although it is unlikely.” What would be the tipping point in finishing the epidemic is a vaccine, even one that is moderately effective.

“Before we didn’t even have the tools,” Fauci says. “Now we have treatment for the individual, treatment as prevention, and we have pre-exposure prophylaxis.” Better implementation can go a long way to improving the situation. “But if you really want to end the epidemic,” he says, “we need an extra tool. It doesn’t have to be a 98 percent [effective] vaccine. But you must prevent infections in a different way along with treatment as prevention and pre-exposure prophylaxis. A vaccine between 50 and 60 percent effective would be enough.”

Recent research advances continue to provide hope there will be such a vaccine. “It is critical to continue to accelerate a robust research effort in that direction while aggressively scaling up the implementation of current treatment and prevention tools,” he concluded in the commentary. “To do anything less would lead to failure, which for HIV is not an option.”

Michael Dumiak reports on global science, public health and technology and is based in Berlin.