synthetic biology biofuels


Building Better Biofuels

Startup LS9 is developing microbes that produce hydrocarbons.
By sai kiran reddy

Stephen del Cardayre, a biochemist and LS9's vice president for research and development.
Credit: Saul Bromberger and Sandra Hoover
While much of the focus is on ethanol, LS9, of San Carlos, CA, is using the relatively new field of synthetic biology to engineer bacteria that can make hydrocarbons for gasoline, diesel, and jet fuel. Hydrocarbon fuels are better suited than ethanol to existing delivery infrastructure and engines, and their manufacture would require less energy. To make biological production of hydrocarbons a reality, the company is bringing together leaders in synthetic biology and industrial biotechnology.
LS9 is at a very early stage: the company was formed in 2005, but its existence was announced only this winter. It plans to engineer microbes to incorporate gene pathways that other microbes, plants, and even animals use to store energy. Other startups, such asAmyris, of Emeryville, CA, and SunEthanol, of Amherst, MA, are also trying to use synthetic biology to develop microorganisms that produce biofuels. Stephen del Cardayre, a biochemist and LS9's vice president for research and development, says LS9 microbes produce and excrete hydrocarbons that are useful as fuels.
Now the company is working to customize the rate of production and the products themselves. e certainly have gone beyond what we think anybody else was even thinking of doing" in terms of producing hydrocarbons from microbes, says George Church, a geneticist at Harvard Medical School and one of LS9's two founders. The other is Chris Somerville, professor of plant biology at Stanford University.
The company has $5 million in funding from Khosla Ventures, of Menlo Park, CA, and Flagship Ventures, of Cambridge, MA. Its acting CEO, Douglas Cameron, is former director of biotechnology research at Cargill and chief scientific officer at Khosla Ventures. Flagship CEO Noubar Afeyan cautions that no one can tell the extent to which any biofuel will displace fossil fuels. "That is a subject of great debate and great prognostication," he says. "The opportunity is so large that I don't have to believe in much more than a few percentage points of market penetration for it to be worth our investment."
The company is looking for areas where synthetic biology's potential to produce specific types of molecules will pay off. This could mean making high-performance jet fuel, Afeyan says, or it could mean creating gasoline that has no pollution-causing sulfur content. Beyond custom-developing hydrocarbons, LS9 foresees licensing its technology. In particular, the company might someday forge agreements with ethanol producers, whose manufacturing plants could be put to more profitable and efficient use making hydrocarbon fuels.
LS9 is counting on the fact that ethanol is not really the best biofuel. Del Cardayre notes that ethanol can't be delivered through existing pipelines. It also contains 30 percent less energy than gasoline, and it must be mixed with gasoline before being burned in conventional engines. LS9's fuels would have none of these disadvantages. What's more, LS9's fuels might be produced more efficiently than ethanol. For example, at the end of ethanol fermentation, the mixture has to be distilled to separate ethanol from water. LS9's products would just float to the top of a fermentation tank to be skimmed off. Overall, the LS9 process consumes about 65 percent less energy than today's ethanol production, the company says.
LS9 now needs to prove that its technology is economical and can produce fuels on a large scale, says Jim McMillan, principal biochemical engineer in the National Renewable Energy Laboratory's Bioenergy Center, based in Golden, CO. "I don't doubt that [making hydrocarbon fuel from microbes] can be done; the question is how quickly and at what cost," he says. LS9 says it hopes to bring its hydrocarbon biofuels to market in four or five years.

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PCR (Polymerase Chain Reaction)

    PCR (Polymerase Chain Reaction)

    PCR is a process of DNA amplification (replication). Polymerase is an enzyme responsible for DNA synthesis, while "Chain Reaction" means exponential growth (at the rate of 2n where n denotes the number of generation) - hence the PCR name. The process is essential for sequencing unique piece of DNA such as those from the genomic specimen, the fossil, or a single hair in a crime scene. Here's a summary of each step in running the PCR (see Figure 07): 1. A target sequence is chosen on the DNA. The sequence had to be known, or at least its two termini. 2. Since DNA replication always runs from the 5' end to the 3' end, two DNA primers were synthesized for each strand. The primer is a small complementary to the 3' end of the original DNA about 20 bp long, it acts as an anchor
    PCRpoint for DNA polymerase and as initiator of the copying process.
    3. Modern technique uses the Taq polymerase (from a microbe in hot springs) to add nucleotide to the new strand. It has the advantage of tolerance to heating up to 94oC - well beyond the 72oC for the extension phase.
    4. All four DNA nucleotide building blocks are added in sufficient quantity.
    5. The sample is heated to a temperature of up to 98oC to separate the complementary strands. This step is called denaturation.
    6. Then the sample is cooled. During the cooling stage, the synthetic primers found complementary sites on the separated DNA strands, whereas the two long DNA strands were unable to find each other because they were present in minute concentration. This process is called primer annealing.
    7. The polymerase extended the two primers in opposite directions. As a result, two daughter DNA appeared.
    8. Initially, the new DNA carries long single-stranded tail. Only at the 3rd cycle

    Figure 07 PCR Process

    of denaturation-annealing-extension do first authentic copy of the molecules appear. The process can make billion copies by the 30th cycle.

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Gel Electrophoresis

    Gel Electrophoresis

    The gel electrophoresis method was developed in the late 1960's. It is a fundamental tool for DNA sequencing. The following outlines steps for its construction (see Figure 05):
    Gel Electrophoresis1. Agarose powder is mixed with electrophoresis buffer (for establishing pH level, and providing ions to support conductivity, usually Tris-acetate-EDTA (TAE) or Tris-borate-EDTA (TBE)) to the desired concentration, then heated in a microwave oven until completely melted. Most commonly, ethidium bromide (a fluorescent dye that intercalates between bases of nucleic acids and allows very convenient detection of DNA fragments in gels) is added to the gel at this point. After cooling the solution to about 60C, it is poured into a casting tray containing a sample comb and allowed to solidify at room temperature. The insert in Figure 05

    Figure Gel Electrophoresis

    shows the effect of agarose concentration on the migration of DNA with 7% resolves longer piece better while the 1.5% is good for the shorter one.
    2. After the gel has solidified, the comb is removed to form wells for the samples.
    The gel, still in its plastic tray, is inserted horizontally or vertically (depending on the design of the apparatus) into the electrophoresis chamber and covered with buffer. Samples containing DNA mixed with loading buffer (which contains something dense, e.g., glycerol to allow the sample to "fall" into the sample wells, and one or two tracking dyes to allow visual monitoring) are then pipeted into the sample wells, the lid and power leads are placed on the apparatus, and a voltage of no more than 5 volts per cm is applied (the cm value is the distance between the two electrodes). 3. In the electrophoresis buffer the DNA dissociates into a negatively charged moiety and a hydrogen ion. Thus the DNA anion will migrate toward the positive electrode. Since the DNA molecules have to wiggle through the microscopic meshes within the gel (called viscosity in physics), the rate of migration depends on their length - the shorter one moves faster, i.e., the mobility is inversely proportional to the log10 of the molecular weight. Now the DNA fragments of different size have been separated into groups as shown in Figure 05. This is an important step toward DNA sequencing, but the identity of the DNA is still unknown. The great length of DNA molecules was the main stumbling block that prevented its sequencing. The problem was resolved by the discovery that bacteria use an enzyme to restrict infection by certain bacteriophages - hence the term restriction enzyme. The restriction enzymes are since used to cut whole piece of DNA into fragments (Figure 06a). Specifically, there are enzymes to cut DNA precisely after an adenosine nucleotide (A) or T, or G, or C.
    Restriction EnzymeAutomated Gel ElectrophoresisThe Maxam-Gilbert method of DNA sequencing separates the DNA sample into four groups each one treated with a specific restriction enzyme for A, T, G, or C. After this, all four groups are placed in the same apparatus for gel electrophoresis. The resulting DNA sequence is shown in Figure 06a. The process can be automated by attaching different fluorescent dye to the end of the DNA fragments in each group and

    Figure 06a Restriction Enzyme
    [view large image]

    Figure 06b Automation[view large image]

    read off by a scanning detector hooking up to a computer (Figure 06b).
    This technique can be used to sequence fragments of DNA up to many hundreds of units. It has since been refined to perfection by the Sanger's method.

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HIV AND AIDS


 HIV, is the virus that causes acquired immune deficiency syndrome (AIDS). The virus weakens a person's ability to fight infections andcancer. People with HIV are said to have AIDS when they develop certain infections or cancers or when their CD4 count is less than 200. CD4 count is determined by a blood test in a doctor's office.
Having HIV does not always mean that you have AIDS. It can take many years for people with the virus to develop AIDS. HIV and AIDS cannot be cured. Although people with AIDS will likely one day die from an AIDS-related illness, there are ways to help people stay healthy and live longer.

How does HIV and AIDS cause illness?

HIV attacks and destroys a type of white blood cell called a CD4 cell. This cell's main function is to fight disease. When a person's CD4 cell count gets low, they are more susceptible to illnesses.

What is AIDS?

AIDS is the final stage of HIV infection. When the immune system CD4 cells drop to a very low level, a person's ability to fight infection is lost. In addition, there are several conditions that occur in people with HIV infection with this degree of immune system failure—these are called AIDS defining illnesses.

How do people get HIV?

According to the Center for Disease Control and Prevention, in the U.S. the estimated number of people with HIV/AIDS is about 1,185,000 with approximately 25% of them unaware of their infection. The estimated number of new cases of HIV is 42,000 each year. A person gets HIV when an infected person's body fluids (blood, semen, fluids from the vagina or breast milk) enter his or her bloodstream. The virus can enter the blood through linings in the mouth, anus or sex organs (the penis and vagina), or through broken skin.
Both men and women can spread HIV. A person with HIV can feel okay and still give the virus to others. Pregnant women with HIV also can give the virus to their babies.
Common ways people get HIV:
  • Sharing a needle to take drugs
  • Having unprotected sex with an infected person
You cannot get HIV from:
  • Touching or hugging someone who has HIV/AIDS
  • Public bathrooms or swimming pools
  • Sharing cups, utensils, or telephones with someone who has HIV/AIDS
  • Bug bites

Who can get HIV?

Anyone can get HIV if they engage in certain activities. You may have a higher risk of getting HIV if you:
  • Have unprotected sex. This means vaginal or anal intercourse without a condom or oral sex without a latex barrier with a person infected with HIV.
  • Share needles to inject drugs or steroids with an infected person. The disease can also be transmitted by dirty needles used to make a tattoo or in body piercing.
  • Receive a blood transfusion from an infected person. This is very unlikely in the U.S. and Western Europe, where all blood is tested for HIV infection.
  • Are born to a mother with HIV infection. A baby can also get HIV from the breast milk of an infected woman.
If you fall into any of the categories above, you should consider being tested for HIV.
Health care workers are at risk on the job and should take special precautions. Some health care workers have become infected after being stuck with needles containing HIV-infected blood or less frequently, after infected blood contact with an open cut or through splashes into the worker's eyes or inside their nose.

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What are the key principles in managing HIV infection?


What are the key principles in managing HIV infection?

First of all, there is no evidence that people infected with HIV can be cured by the currently available therapies. In fact, individuals who are treated for years and are repeatedly found to have no virus in their blood experience a prompt rebound in the number of viral particles when therapy is discontinued. Consequently, the decision to start therapy must balance the risk versus the benefits of treatment. The risks of therapy include the short- and long-term side effects of the drugs, described in subsequent sections, as well as the possibility that the virus will become resistant to the therapy which can limit options for future treatment.
A major reason that resistance develops is the patient's failure to correctly follow the prescribed treatment, for example, by not taking the medications at the correct time. If virus remains detectable on any given regimen, resistance eventually will develop. Indeed, with certain drugs, resistance may develop in a matter of weeks, such as with lamivudine (Epivir, 3TC),emtricitabine (Emtriva, FTC), and the drugs in the class of nonnucleoside analogue reverse transcriptase inhibitors (NNRTI) such asnevirapine (Viramune, NVP), delavirdine(Rescriptor, DLV), and efavirenz (Sustiva, EFV). Thus, if these drugs are used as part of a combination of drugs that does not suppress the viral load to undetectable levels, resistance will develop rapidly and the treatment will lose its effectiveness. In contrast, HIV becomes resistant to certain other drugs, such aszidovudine (Retrovir, AZT), stavudine (Zerit, D4T), and protease inhibitors (PIs), over months. In fact, for some PIs whose effects are enhanced by giving them in combination with the PI,ritonavir (Norvir, RTV) to delay their clearance by the body, resistance appears to be markedly delayed. These drugs are discussed in more detail in subsequent sections, but it is important to note that when resistance develops to one drug, it often results in resistance to other related drugs, so called cross-resistance. Nevertheless, HIV-infected individuals must realize that antiviral therapy can be and typically is very effective. This is the case even in those who have a low CD4 cell count and advanced disease, as long as drug resistance has not developed.
Factors to consider before starting antiviral therapy
One of the most controversial areas in the management of HIV disease is deciding the best time to start antiviral treatment. Clearly, therapy during the mildly symptomatic stage of the disease delays progression to AIDS, and treating individuals with AIDS postpones death. Consequently, most experts have long agreed that patients who have experienced complications of HIV disease, such as oral thrush (yeast infection in the mouth), chronic unexplained diarrhea, fevers, weight loss, opportunistic infections, or dementia (for example, forgetfulness) should be started on antiviral treatment even if the symptoms are mild. In patients who do not have symptoms, however, there is more uncertainty. Most recommendations for this group are based on the predictors of clinical progression, such as the number of CD4 cells. One can envision that as treatments become easier to take, better tolerated, and increasingly effective, therapy will begin to be started earlier in the course of infection.
When to start antiviral therapy
Guidelines for starting antiviral therapy have been proposed by panels of experts from several groups including the DHHS and IAS-USA. They recommend treating all patients who have symptoms and those who have CD4 cell counts of less than 350 cells per mm3. Recent data supporting even earlier initiation of therapy includes analyses of groups of patients followed over time. Although the data is imperfect, a recent study showed that those who started treatment with CD4 cells greater than 500 cells per mm3 actually were less likely to die than those who did not start treatment until their CD4 cells declined to less than 500 cells/mm3. In addition, there is increasing evidence that ongoing viral replication, even in the setting of high CD4 cells may be associated with damage to the brain, kidneys, heart, and possibly even liver. Along with these studies arguing for earlier treatment, there is growing evidence that currently used treatments are usually very well tolerated and effective in suppressing viral load. Guidelines will continue to change with time, but for now, the emphasis should be on discussing all of the potential benefits and risks of therapy and deciding when is best for each individual. Regardless, all agree that HIV is generally a slowly progressive disease, and therapy rarely needs to be started abruptly. Therefore, there usually is time for each patient to carefully consider options prior to starting treatment.
Before starting treatment, patients must be aware of the short- and long-term side effects of the drugs, including the fact that some long-term complications may not be known. Patients also need to realize that therapy is a long-term commitment and requires consistent adherence to the drugs. In addition, clinicians and patients should recognize thatdepression, feelings of isolation, substance abuse, and side effects of the antiviral drugs can all be associated with the failure to follow the treatment program.
Initial therapy for HIV
Guidelines for using antiviral therapy have been developed and are updated on a regular basis by an expert panel assembled by the DHHS, the IAS-USA panel, and others. The DHHS guidelines are available at http://www.hivatis.org. The most recent IAS-USA guidelines were published in the Journal of the American Medical Association (JAMA) in the summer of 2008.
Antiviral treatment options have primarily included combinations of two nucleoside analogue reverse transcriptase inhibitors (NRTI), often referred to as "nucs," and one PI, typically with a low dose of RTV, a PI used at low doses to increase the level of the principle PI being used, so called "boosting." Alternative, preferred options include the use of two NRTIs with a nonnucleoside analogue reverse transcriptase inhibitor (NNRTI), the latter often called "non-nucs." These NNRTI-containing combinations generally are easier to take than PI-containing combinations and tend to have different side effects. Recently, NRTIs were combined with the integrase inhibitor raltegravir (Isentress, RAL) with very good viral suppression and tolerability. This novel combination has now been approved by the Food and Drug Administration as another treatment option for those initiating therapy for the first time.
Nucleoside and nucleotide analogue reverse transcriptase inhibitors
NRTIs block an enzyme of the HIV called reverse transcriptase that allows HIV to infect human cells, particularly CD4 T cells or lymphocytes. Reverse transcriptase converts HIV genetic material, which is RNA, into human genetic material, which is DNA. The human-like DNA of HIV then becomes part of the infected person's own cells, allowing the cell to produce RNA copies of the HIV that can then go on to attack other not yet infected cells. Thus, blocking reverse transcriptase prevents HIV from taking over (infecting) human cells.
In general, most antiviral regimens for HIV disease contain a backbone of at least two NRTIs. The NRTIs include ZDV, d4T, ddI, zalcitabine (HIVID, ddC), 3TC, FTC, abacavir(Ziagen, ABC) or TDF. The NRTIs FTC and 3TC are highly related compounds and, although data is somewhat limited, most experts agree that they probably can be used interchangeably. That said, many combinations of NRTIs can be used together, with current guidelines generally recommending the fixed-dose combination of TDF with FTC with alternatives being the fixed-dose combinations of ABC/3TC or ZDV/3TC. Other options would include ddI plus 3TC or FTC. ABC has been associated with severe allergic reaction in approximately 5% of patients. Recent studies have shown that a blood test can be performed to determine who is at risk for this reaction so that the drug can be avoided in these individuals and be used in others with greater confidence that there will not be such a reaction.
Usual dosing schedule and meal restrictions for NRTIs

ZDV

d4T

ddl

ddC

3TC

ABC

TDF

FTC

Dose in each pill (mg)
30030 or 40100 or 4000.75150 or 300300300200
Schedule1 twice/day1 twice/day
2 (100) twice/day or
1 (400) once/day
1 thrice/day1 (150) twice/day or 1(300) once/day1 twice/day or 2 once/day1 once/day1 once/day
Meal restrictionsNoneNone
30 minutes before or 60 minutes after a meal
NoneNoneNoneNoneNone
ZDV, zidovudine; d4T, stavudine; ddI, didanosine; ddC, zalcitabine; 3TC, lamivudine; ABC,abacavir; TDF, tenofovir; FTC, emtricitabine.
The following are available fixed-dose combination pills of NRTIs:
  • ZDV/3TC (300 mg/150 mg) as Combivir; one twice per day
  • ZDV/3TC/ABC (300 mg/150 mg/300 mg) as Trizivir; one twice per day
  • ABC/3TC (600 mg/300 mg) as Epzicom; one per day
  • TDF/FTC (300 mg/200 mg) as Truvada; one per day
These are standard doses for average-sized adults, and dosing may vary depending upon the weight of a patient. When TDF is taken with ddI, the standard ddI dose should be reduced to 250 mg per day and can be taken with food.
Nonnucleoside analogue reverse transcriptase inhibitors
Like NRTIs, NNRTIs block the reverse transcriptase enzyme preventing uninfected cells from becoming infected.
NNRTIs include NVP, DLV, EFV and the recently approved etravirine (Intelence, ETR). ETR was developed specifically to be an option for patients that have developed resistance to the earlier drugs in the class. NVP, DLV, and EFV are typically used with two NRTIs, and ETR is primarily being used as part of regimens for those with a history of different types of treatment to which they have developed resistance.
Usual dosing schedule and meal restrictions for NNRTIs


NVP

 DLV

EFV

ETR

Dose in
each pill (mg)
200200600100
Schedule
1 twice/day
(start with 1 once/day
for first 14 days)
2 thrice/day1 once/day2 twice/day


Meal restrictions


None


None


Avoid high-fat meals


After meals
NVP, nevirapine; DLV, delavirdine; EFV, efavirenz; ETR, etravirine.
For people without a history of drug resistance, there is a very effective fixed-dose combination pill that includes TDF with FTC and EFV as a single pill that can be taken once per day.
Protease inhibitors
PIs block the action of an HIV enzyme called protease that allows HIV to produce infectious copies of itself within HIV-infected human cells. Thus, blocking protease prevents HIV in already-infected cells from producing HIV that can infect other, not yet infected cells.
PIs include
Each of these drugs has been shown to effectively reduce the viral load when used in combination with other active drugs.
Usual dosing schedule and meal restrictions for PIs

SQV+IDVNFVFPVLPV/rATVTPVDRV
Dose in each pill (mg)500400625700200/50200 or 300250400 or 600
Schedule21twice/day2 every 8 hours
2 twice/day
2 twice/day or with RTV22 twice/day or 4 once/day2 (200) or 1 (300) with RTV3once/day24twice/day8005once/day or 600 twice/day
Meal restrictionsWith large meals
1 hour before or 2 hours after meals, or with low-fat meals
With mealsNoneWith mealsWith mealsWith mealsWith meals
SQV, saquinavir; IDV, indinavir; NFV, nelfinavir; FPV, fosamprenavir; LPV/r, lopinavir plus ritonavir; ATV, atazanavir; TPV, tipranavir; DRV, darunavir.
1Administered with RTV at a dose of 100 mg twice/day.2FPV can be given without RTV in patients without resistance to PIs or at a dose of 1,400 mg once daily with either 100 mg or 200 mg of RTV once daily. In treatment-experienced patients, FPV is given at a dose of 700 mg twice daily with RTV 100 mg twice daily.3ATV can be given alone at a dose of 400 mg once daily or at a dose of 300 mg once daily with RTV 100 mg once/daily.4TPV is always given at a dose of 500 mg twice/daily with RTV 200 mg twice daily.5DRV can be given to those with a history of drug resistance at a dose of 600 mg twice daily with 100 mg RTV twice daily. For those without resistance, it can be given at a dose of 800 mg (two 400 mg tablets) with 100 mg RTV once daily.
Although RTV is approved for treatment of HIV-infected patients at a dose of 600 mg twice daily, it is virtually never used at this dose because of severe side effects. Because of this, it is not included in the above table. However, PIs are frequently dosed with low doses of RTV. RTV delays the clearance of the other drugs from the system, making them easier to take and more effective. The dose of RTV varies depending upon which drugs it is being taken with and how it is being administered. The only PI that is not substantially affected by RTV is NFV.
LPV/r comes coformulated as Kaletra while all other RTV-containing regimens require taking RTV along with the other PI. In the case of TPV, RTV must be given as 200 mg with each dose of TPV twice per day. In contrast, ATV can be given without RTV at a dose of two 200 mg capsules once daily or 300 mg with 100 mg RTV once daily. The latter should always be used in PI-experienced subjects and when used in combination with TDF or NNRTIs which can reduce the drug levels of ATV. Similarly, FPV is also used differently in PI-naïve and experienced individuals. In treatment-naïve individuals, it can be given as two 700 mg tablets twice daily or two 700 mg tablets (1,400 mg total) with either 100 or 200 mg RTV, all once daily. In treatment-experienced patients, or when used with NNRTIs, it should be given as one 700 mg tablet with 100 mg RTV, both twice daily. The most recently approved of the PIs is DRV which was initially used exclusively in treatment-experienced patients with drug-resistant virus. In this setting, it is given as 600 mg with 100 mg RTV, both given twice daily. More recently, DRV was approved for those who have never been treated before given at a dose of two 400 mg tablets (800 mg total) once daily with 100 mg of RTV once daily.
Fusion inhibitors
A fusion inhibitor blocks an early step in the viral life cycle. Enfuvirtide (Fuzeon, T-20) attaches to the envelope surrounding the virus and prevents it from entering the CD4 cells. This prevents the infection of CD4 cells by HIV. T-20 is the first approved drug in this class. It is given as a twice daily subcutaneous injection (90 mg). It is used primarily in individuals who have developed resistance to other classes of drugs in order to create a new potent combination. Like all other antivirals, it is most useful in those taking other active drugs at the same time in order to optimize the chance of getting viral loads to undetectable levels and to prevent the development of drug resistance.
CCR5 antagonist
The first available drug in this class is called maraviroc (Selzentry, MVC), which was recently approved for use in combination therapy in treatment-experienced patients with drug-resistant virus who do not have detectable CXCR4-using virus as determined by a tropism assay. This is a unique drug in a new class that blocks viral entry by interacting with the CCR5 molecule on the surface of the CD4 cell. It is known that HIV first binds to the CD4 molecule on the surface of CD4 cells and then connects with the CCR5 or CXCR4 molecule. Only after this second step is the virus able to enter the cell. The CCR5 antagonist prevents viruses that use CCR5 from getting into the cell. What is unique about this drug compared to others is that 20%-50% of patients have viruses that are able to use the CXCR4 receptor. In these cases, CCR5 antagonists do not appear to be active at suppressing virus. Therefore, in order to know if the drug will work for a given patient, a new test needs to be performed, the so called "tropism" assay. This test will tell the provider and patient whether there is virus that uses CXCR4, in which case the patient would not be a candidate for MVC, or if they only have viruses that use CCR5, in which case MVC should be an active drug. Without tropism results, it is impossible to know whether MVC will be an active drug for a given patient.
MVC is dosed at either 300 mg or 150 mg twice daily, depending upon what other drugs it is given with. If the patient is taking any RTV, then they would usually receive the 150 mg dose. If RTV is not being used as part of the regimen, they would generally receive the 300 mg dose and sometimes even higher if it is being used with drugs like ETR. HIV providers are aware that whenever using any anti-HIV medications attention must be given to possible drug interactions.
Integrase inhibitor
The first available drug in this class is RAL and represents a new drug in a new class that appears to be very potent at suppressing HIV in all patients who have never been on this drug or other integrase inhibitors in development. It was initially approved for treatment-experienced patients with drug-resistant virus. It is also now approved for those starting therapy for the first time. The approved dose of RAL is 400 mg twice daily.
Drugs in development
There are many drugs currently in development that may simplify therapy and provide important options for those who have developed extensive drug resistance. Drugs that show promise in early clinical trials are often made available by the manufacturer with approval of the Food and Drug Administration (FDA), to certain individuals. In particular, these drugs are used in individuals no longer responding or able to tolerate currently available agents. The most promising new drugs at this time are those in existing classes, such as a new integrase inhibitor, CCR5 antagonist, and NNRTI.
Side effects of HIV therapy
There are many potential side effects associated with antiviral therapies. The most common ones for each class of drug are summarized in readily available product information. Some specific toxicities are summarized by class below.
NRTIs
Most NRTIs can cause mild nausea and loose stools. In general, these symptoms resolve with time.
ZDV has been associated with decreased production of blood cells by the bone marrow, most often causing anemia, and occasionally hyperpigmentation (most often of the nails).
D4T can damage nerves and cause peripheral neuropathy, a neurological condition with numbness and/or tingling of the feet and hands, and inflammation of the pancreas (pancreatitis) that causes nausea, vomiting, and mid upper abdominal pain.
DDI also causes pancreatitis and, to a lesser extent, peripheral neuropathy. Peripheral neuropathy can become permanent and painful, and pancreatitis can be life-threatening if therapy is not discontinued. The drug ddC also is associated with peripheral neuropathy as well as oral ulcers.
ABC can cause a hypersensitivity reaction during the first two to six weeks of therapy in approximately 5% of individuals. The hypersensitivity reaction most often causes fever and other symptoms, such as muscle aches, nausea, diarrhea, rash, or cough. The symptoms generally get worse with each dose of ABC and, if suspected, therapy must be discontinued and never restarted for fear of developing a life-threatening reaction. There is now a simple blood test that can be performed to determine whether a patient is at risk for developing the hypersensitivity reaction. If the test is positive, the patient should never receive this medication.
TDF is generally well tolerated although there may be rare kidney damage.
FTC is also well tolerated except for the occasional development of hyperpigmentation, most often on the palms and soles. This hyperpigmentation occurs more frequently in people of color.
Although all NRTIs can be associated with lactic acidosis (a serious condition in which lactic acid accumulates in the blood), it may occur more often with some drugs, such as d4T. Although this complication of treatment is rare, it can be severe and life-threatening. Early symptoms of lactic acidosis are nausea, fatigue, and sometimes, shortness of breath. Lactic acidosis needs to be watched for and, if suspected, requires that therapy be discontinued until symptoms and laboratory test abnormalities resolve.
There has been a great deal of attention given to the more recently identified problem of "lipodystrophy." Individuals suffering from this syndrome can be categorized as having lipohypertrophy (fat accumulation) syndromes, such as the "buffalo hump" on the back of the neck, breast enlargement, or increased abdominal girth. Others primarily suffer from lipoatrophy with fat loss under the skin with complaints of prominent veins on the arms and legs, sunken cheeks, and decreased gluteal (buttock) size. These syndromes appear to be related to multiple factors including, but not limited to, drug therapy. The NRTIs appear to be most closely linked to lipoatrophy, in particular D4T and to a lesser extent ZDV. In fact, some studies have suggested slow accumulation of fat in those who modify the NRTI component of their regimen. Some NRTIs also have been linked to elevation in lipid (fat) levels in the blood. While switching therapy is always a consideration in those experiencing potential drug-related toxicity, this should only be done under the careful supervision of an experienced HIV provider.
NNRTIs
The most common side effect associated with NNRTIs is a rash, typically occurring during the first weeks of therapy. This is most common in individuals treated with NVP. In this case, the overall risk of rash is reduced if therapy is started as a single, 200 mg NVP pill once per day during the first two weeks before increasing to the full dose of 200 mg twice per day. If the rash is mild, therapy usually can be continued if antihistamines are given, and if the rash resolves, treatment with the NNRTI can be continued. If the rash is severe, associated with liver inflammation or blisters, changes in the mouth or around the eyes, or with high fevers, therapy with the NNRTI usually needs to be discontinued. Decisions regarding continuing or stopping treatment need to be made with the primary-care provider. In some patients, NVP can cause a severe allergic reaction characterized by fever, rash, and severe liver inflammation. Recent data suggests that the groups at the greatest risk for the severe reaction are those with stronger immune systems, such as HIV-uninfected people given this treatment after an exposure to HIV, women with CD4+ T cells >250 cells per mm3and men with CD4+ T cells >400 cells per mm3. There is also likely to be increased risk in pregnant women and individuals with other underlying liver diseases. Consequently, NVP probably should not be used in any of these groups, or if used, used with caution. In addition, whenever NVP is started, liver tests that are markers for liver inflammation should be monitored at regular intervals during the first several months of treatment.
Side effects associated with EFV are mostly dizziness, confusion, fatigue, and vivid dreams. These tend to be most prominent during the first weeks of therapy and then often decrease in severity. It is generally recommended that EFV be taken at bedtime so that the patient is asleep during the time dizziness and confusion may be most severe. It is also noteworthy that there may be an increased risk of depression associated with the use of this drug, and it should be used with caution in those with poorly managed depression. Rash and liver inflammation can occur with both EFV and DLV, and these drugs may also be linked to abnormalities of lipids in the blood.
The most common side effect reported with the most recently approved NNRTI, ETR, is rash and it was generally mild and rarely required that medications needed to be stopped.
PIs
There are currently nine approved PIs that all have distinct toxicities. The most common side effects associated with these drugs are nausea and diarrhea, which occur more often with some PIs than others. For example, diarrhea is more common with NFV than other PIs but can occur with any and all drugs in this class. Many of the drugs in this class also increase blood lipid levels, some more than others with ATV and possibly DRV appearing to have less effect on lipids than other drugs in the class. Other unique toxicities associated with various PIs are kidney stones with IDV and ATV and increased blood bilirubin levels with IDV and ATV. Some of these drugs also have been associated with elevations in blood sugar levels and bleeding in hemophiliacs. Finally, little is known regarding the role these drugs may play in the development of lipodystrophy.
Fusion inhibitors
The only drug in this class is T-20, which is administered as a twice daily subcutaneous injection. The most common side effect is redness and pain at the site of injection. Rarely, infection can occur at the injection site. There also are reports of generalized allergic reactions.
CCR5 antagonist
Although there were some early concerns of liver inflammation for drugs in this class, MVC appeared to be well tolerated in clinical trials without any specific toxicities attributable to the drug. However, it is a new drug in a new class and the first to actually target the cell. For these reasons, longer follow-up from clinical trials and those followed in the clinic will be very important for assessing the overall safety of the drug.
Integrase inhibitor
RAL has not been strongly linked to any specific side effect in clinical trials. However, there have been some cases of muscle problems that need to be watched for when starting this or any new medications. As with all new medications, more data will come from extended follow-up of patients in the clinic and in clinical trials.
Monitoring antiviral therapy
The goals of antiviral therapy are to enhance immunity and delay or prevent clinical advancement to symptomatic disease without inducing important side effects or selecting for drug resistant virus. Currently, the best marker of a drug's activity is a decrease in the viral load.
Ideally, prior to initiating treatment, the viral load and the CD4 cell count should be checked and the viral load test then repeated after approximately four weeks of treatment. If the patient is beginning a regimen that includes two to three drugs for which the patient's virus does not appear to be resistant, it is expected that the amount of virus should decrease by at least 100-fold during this interval. The ultimate goal is for the viral load to decrease to undetectable levels which should occur by approximately 24 weeks. Those that are not having an appropriate response to therapy need to be questioned to make sure that they are taking their medications correctly, and if not, why. If the viral load is not going to undetectable levels and the patient is taking the medications correctly, then it is likely that there is a resistant virus to some of the medications. Drug-resistance testing then should be performed and the patient managed as described in the next section
Viral load increasing while on HIV therapy
If the patient does suppress their virus to undetectable levels on antiviral therapy but then develops detectable virus, several things should be considered. First, it must be established that the patient is taking the medications correctly. If they are missing doses, then every effort must be made to understand why this is happening and correct the situation, if possible. If the poor adherence is a result of drug side effects, efforts should be directed toward managing the side effects or changing to a better-tolerated regimen. If poor adherence is occurring because of the medication schedule of dosing, new strategies should be discussed such as placing medications in a pillbox, associating the dosing with certain daily activities such as tooth brushing or possibly changing the regimen. Finally, if the reason for poor adherence is depression, substance abuse, or another personal issue, these issues need to be addressed and managed.
It is important to remember that sometimes, for reasons not entirely understood, the viral load can briefly increase. Unexpected increases, therefore, necessitate repeated testing of the viral load before any clinical decisions are made. If, however, the viral load is continually detected despite proper adherence to the prescribed therapy, serious consideration must be given to the possibility that the virus has become resistant to one or more of the medications being given. There is now an abundance of data showing that the use of drug resistance tests can improve the response to a follow-up regimen. Testing can be used to determine if an individual's HIV has become resistant to one or more of the drugs that are being taken. There are currently two main types of resistance tests available in the clinic: one that is called a genotype and the other a phenotype assay. The former looks for mutations in the virus and the latter the actual amount of drug it takes to block infection by the patient's virus. The genotype test is very helpful in those being screened for the presence of resistant virus prior to initiating treatment and those experiencing viral rebound on one of their first treatment regimens. The phenotype test is particularly useful in those who are highly treatment-experienced and have substantial amounts of drug resistance. The information derived from these tests, along with a tropism test will ultimately tell the provider which of the many approved drugs are likely to be fully active against the specific patient's virus. Using this information, the goal is to include at least two and ideally three fully active drugs in the next regimen in order to optimize the chances of suppressing the viral load to undetectable levels.
Missing doses or stopping antiviral therapy
It is strongly advised that individuals on an antiviral regimen not miss any doses of their medications. Unfortunately, life is such that doses often are missed. Reasons for missing doses range from just forgetting to take the medication, leaving town without the medication, or because of a medical emergency, such as the need for urgent surgery. For example, after an appendectomy for acute appendicitis, a patient may not be able to take oral medication for up to several days. When a dose is missed, the patient should contact his or her physician without delay to discuss the course of action. The options in this situation are to take the missed doses immediately or simply resume the drugs with the next scheduled dose.
Although every missed dose increases the chance that the virus will develop resistance to the drugs, a single missed dose should not be cause for alarm. On the contrary, it is an opportunity to learn from the experience and determine why it happened, if it is likely to happen again, and what can be done to minimize missing future doses. Furthermore, if a patient cannot resume medication for a limited time, such as in a medical emergency, there still is no cause for alarm. In this circumstance, the patient should work with their HIV provider to restart therapy as soon as is feasible. Stopping antivirals is associated with some risks of developing drug resistance, and those who wish to stop therapy for any one of a number of reasons should discuss this with their health-care provider in advance to establish the best strategy for safely accomplishing this.

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