Given the deadly global rampage that HIV has been on for the past few decades, you’re all probably familiar with the virus. But you may not be aware that there are two types of HIV—HIV-1 and HIV-2—with the former being significantly more prevalent worldwide. The most common type of HIV-1 is then further divided into distinct subtypes, some of which are associated with a more rapid progression to AIDS. If these different viruses meet in an infected person, for example if someone infected with one subtype is exposed to a different one, they can exchange bits of their genetic material to create a new virus.
One of these so called “circulating recombinant forms” is currently spreading through Cuba, and it’s unfortunately extremely aggressive. Individuals infected with this hybrid virus, which is a mix of three different HIV-1 subtypes, progress to AIDS more than three times faster than average. Now, scientists have scrutinized this particularly pathogenic strain, which has yielded insight into the traits that have bestowed it with this deadly efficiency. The findings have been published in EBioMedicine.
Before HIV can get inside our cells, it first needs to bind to receptors on the surface called CD4. While this is an essential first step, it’s insufficient to get the virus inside. This is where anchoring points, called coreceptors, come in, which HIV also has to latch onto to gain entry. There are two coreceptors, CCR5 and CXCR4, and around 90% of newly transmitted HIV uses the former.
CXCR4-using viruses emerge in around 50% of individuals, but this usually takes around five years from infection. These viruses are associated with a more pronounced depletion of immune cells, but whether this shift in coreceptor preference is a cause or consequence of disease progression is unknown. Interestingly, however, the aggressive recombinant currently spreading through Cuba starts to use CXCR4 very early on in infection, and researchers think this is likely contributing to the observed rapid progression to AIDS.
To find this out, researchers examined 73 recently infected patients in Cuba, 52 who had rapidly progressed to AIDS within three years and 21 without AIDS. Then, they compared the blood of these individuals with 22 patients who had progressed to AIDS after the period typically expected, which is around 10-15 years without treatment.
They found that all those who had progressed to AIDS within three years of infection were infected with a recombinant called CRF19, which is a mixture of subtypes A, D and G. Interestingly, infection with A/D recombinants has previously been reported to result in rapid progression to AIDS, but no CRFs had been exclusively associated with rapid progression. Furthermore, those infected with CRF19 had abnormally high levels of an immune response molecule called RANTES, which acts by binding to CCR5. Without this coreceptor available for binding, CRF19 may have been forced to bypass that anchor point and go straight for CXCR4. Since the switch to CXCR4 usage is associated with progression to AIDS, this could explain why those infected with CRF19 developed AIDS so early on.
Another reason that CRF19 might be so pathogenic is that it has an enzyme, called protease, from subtype D, which is known to be very efficient. This enzyme helps the virus form mature particles, which is an essential stage in the virus life cycle.
A team led by scientists from The Scripps Research Institute (TSRI) and the International AIDS Vaccine Initiative (IAVI) has unveiled a new technique for vaccine design that could be particularly useful against HIV and other fast-changing viruses.
The report, which appears March 28, 2013, in Science Express, the early online edition of the journal Science, offers a step toward solving what has been one of the central problems of modern vaccine design: how to stimulate the immune system to produce the right kind of antibody response to protect against a wide range of viral strains. The researchers demonstrated their new technique by engineering an immunogen (substance that induces immunity) that has promise to reliably initiate an otherwise rare response effective against many types of HIV.
“We’re hoping to test this immunogen soon in mice engineered to produce human antibodies, and eventually in humans,” said team leader William R. Schief, who is an associate professor of immunology and member of the IAVI Neutralizing Antibody Center at TSRI.
Seeking a Better Way
For highly variable viruses such as HIV and influenza, vaccine researchers want to elicit antibodies that protect against most or all viral strains — not just a few strains, as seasonal flu vaccines currently on the market. Vaccine researchers have identified several of these broadly neutralizing antibodies from long-term HIV-positive survivors, harvesting antibody-producing B cells from blood samples and then sifting through them to identify those that produce antibodies capable of neutralizing multiple strains of HIV. Such broadly neutralizing antibodies typically work by blocking crucial functional sites on a virus that are conserved among different strains despite high mutation elsewhere.
However, even with these powerful broadly neutralizing antibodies in hand, scientists need to find a way to elicit their production in the body through a vaccine. “For example, to elicit broadly neutralizing antibodies called VRC01-class antibodies that neutralize 90 percent of known HIV strains, you could try using the HIV envelope protein as your immunogen,” said Schief, “but you run into the problem that the envelope protein doesn’t bind with any detectable affinity to the B cells needed to launch a broadly neutralizing antibody response.”
To reliably initiate that VRC01-class antibody response, Schief and his colleagues therefore sought to develop a new method for designing vaccine immunogens.
From Weak to Strong
Joseph Jardine, a TSRI graduate student in the Schief laboratory, evaluated the genes of VRC01-producing B cells in order to deduce the identities of the less mature B cells — known as germline B cells — from which they originate. Germline B cells are major targets of modern viral vaccines, because it is the initial stimulation of these B cells and their antibodies that leads to a long-term antibody response.
In response to vaccination, germline B cells could, in principle, mature into the desired VRC01-producing B cells — but natural HIV proteins fail to bind or stimulate these germline B cells so they cannot get the process started. The team thus set out to design an artificial immunogen that would be successful at achieving this.
Jardine used a protein modeling software suite called Rosetta to improve the binding of VRC01 germline B cell antibodies to HIV’s envelope protein. “We asked Rosetta to look for mutations on the side of the HIV envelope protein that would help it bind tightly to our germline antibodies,” he said.
Rosetta identified dozens of mutations that could help improve binding to germline antibodies. Jardine then generated libraries that contained all possible combinations of beneficial mutations, resulting in millions of mutants, and screened them using techniques called yeast surface display and FACS. This combination of computational prediction and directed evolution successfully produced a few mutant envelope proteins with high affinity for germline VRC01-class antibodies.
Jardine then focused on making a minimal immunogen — much smaller than HIV envelope — and so continued development using the “engineered outer domain (eOD)” previously developed by Po-Ssu Huang in the Schief lab while Schief was at the University of Washington. Several iterative rounds of design and selection using a panel of germline antibodies produced a final, optimized immunogen — a construct they called eOD-GT6.
A Closer Look
To get a better look at eOD-GT6 and its interaction with germline antibodies, the team turned to the laboratory of Ian A. Wilson, chair of the Department of Integrative Structural and Computational Biology and a member of the IAVI Neutralizing Antibody Center at TSRI.
Jean-Philippe Julien, a senior research associate in the Wilson laboratory, determined the 3D atomic structure of the designed immunogen using X-ray crystallography — and, in an unusual feat, also determined the crystal structure of a germline VRC01 antibody, plus the structure of the immunogen and antibody bound together.
“We wanted to know whether eOD-GT6 looked the way we anticipated and whether it bound to the antibody in the way that we predicted — and in both cases the answer was ‘yes’,” said Julien. “We also were able to identify the key mutations that conferred its reactivity with germline VRC01 antibodies.”
Mimicking a Virus
Vaccine researchers know that such an immunogen typically does better at stimulating an antibody response when it is presented not as a single copy but in a closely spaced cluster of multiple copies, and with only its antibody-binding end exposed. “We wanted it to look like a virus,” said Sergey Menis, a visiting graduate student in the Schief laboratory.
Menis therefore devised a tiny virus-mimicking particle made from 60 copies of an obscure bacterial enzyme and coated it with 60 copies of eOD-GT6. The particle worked well at activating VRC01 germline B cells and even mature B cells in the lab dish, whereas single-copy eOD-GT6 did not.
“Essentially it’s a self-assembling nanoparticle that presents the immunogen in a properly oriented way,” Menis said. “We’re hoping that this approach can be used not just for an HIV vaccine but for many other vaccines, too.”
The next step for the eOD-GT6 immunogen project, said Schief, is to test its ability to stimulate an antibody response in lab animals that are themselves engineered to produce human germline antibodies. The difficulty with testing immunogens that target human germline antibodies is that animals typically used for vaccine testing cannot make those same antibodies. So the team is collaborating with other researchers who are engineering mice to produce human germline antibodies. After that, he hopes to learn how to drive the response, from the activation of the germline B cells all the way to the production of mature, broadly neutralizing VRC01-class antibodies, using a series of designed immunogens.
Schief also hopes they will be able to test their germline-targeting approach in humans sooner rather than later, noting “it will be really important to find out if this works in a human being.”
The first authors of the paper, “Rational HIV immunogen design to target specific germline B cell receptors,” were Jardine, Julien and Menis. Co-authors were Takayuki Ota and Devin Sok of the Nemazee and Burton laboratories at TSRI, respectively; Travis Nieusma of the Ward laboratory at TSRI; John Mathison of the Ulevitch laboratory at TSRI; Oleksandr Kalyuzhniy and Skye MacPherson, researchers in the Schief laboratory from IAVI and TSRI, respectively; Po-Ssu Huang and David Baker of the University of Washington, Seattle; Andrew McGuire and Leonidas Stamatatos of the Seattle Biomedical Research Institute; and TSRI principal investigators Andrew B. Ward, David Nemazee, Ian A. Wilson, and Dennis R. Burton, who is also head of the IAVI Neutralizing Center at TSRI.
Joseph Jardine, Jean-Philippe Julien, Sergey Menis, Takayuki Ota, Oleksandr Kalyuzhniy, Andrew McGuire, Devin Sok, Po-Ssu Huang, Skye MacPherson, Meaghan Jones, Travis Nieusma, John Mathison, David Baker, Andrew B. Ward, Dennis R. Burton, Leonidas Stamatatos, David Nemazee, Ian A. Wilson, and William R. Schief. Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors. Science, 28 March 2013 DOI: 10.1126/science.1234150
The discovery of the antibiotics by the middle of the 20th century seemed to have doomed the human pathogens. They proved effective against many bacteria and fungi causing hospital infections, like meningitis, pneumonia and scarlet fever, which before were deadly. But antibiotics cannot attack viruses, like HIV or flu virus; many cause allergies and kill many beneficial microorganisms.
The under use of antibiotics (when a patient does not complete treatment because he/she feels better) cause the emergence of resistant strains, as not all the bacteria are killed. Their abuse is also harmful. In livestock they induce an accelerated growth, and this cause an increase in the microbial resistance. This can leave us without antibiotics.
Massive vaccination campaigns eliminated to the end of the 20th century smallpox and today polio leave paralyzed less than 1,000 children annually (in 1988 more than 1,000 per day), and has remained active in less than 10 countries. Sanitation has eliminated cholera, whose bacterium is transmitted through infested water, from many places. Better food, life style, medical care and laws controlling food manipulation have reduced infection diseases in many places.
In the 21st century, there are still infections against which we are defenseless and which, despite all the medical advances, bringing advantages more to developed nations, still kill millions of people every year. Poverty, war, hunger, lack of health infrastructure and sanitation, immigration, trade, globalization contribute to the spread of the diseases. In the last years, outbreaks of ebola, cholera, pest, meningitis, SARS and bird flu have been witnessed. These are infectious diseases that have produced and produce a lot of victims around the world.
(also called bubonic plague) outbroke in Europe in 1347, when a boat coming from Crimea docked at Mesina, Sicily. Besides its load, the ship transported the pest, which soon spread throughout whole Italy. It was like the end of the days for Europe. In four years, this bacterium killed 20 to 30 million Europeans, about one third of the continent’s population. Even the remote Iceland was struck. In the Extreme East, China dwindled from 123 million inhabitants at the beginning of the 13th century to just 65 million during the 14th century, because of the pest and the hunger.
The pest bacterium is transmitted by fleas and usually, the infection jump from rats to humans.
This catastrophe has not match in the human history. 25 to 50 % of the inhabitants of Europe, North Africa and certain Asian areas died then.
Knowing the cause of the pandemic helped: in 1907 an outbreak of bubonic plague in San Francisco produced just several victims, as the authorities started a massive campaign for exterminating the rats, while in 1896 an outbreak in India caused 10 million dead in 12 years, as the cause was not known.
Americas escaped of the Black Death because of the isolation. But when discovered, the smallpox struck. In 1518 an outbreak of smallpox in the Haiti island left just 1,000 of the Native Indians. 100 years after the discovery of America by Columbus, 90 % of its native population have died of smallpox. Mexico passed from 30 million to 3 million inhabitants, Peru from 8 million to 1 million.
About 1,600, when the first European colonists reached Massachusetts, found it practically uninhabited, as smallpox had killed almost all local Indians.
It is believed that along the history, smallpox killed more humans that all the wars of the 20th century together. Since 1914 to 1977 smallpox killed 300 to 500 million people. By 1970, smallpox still killed 2 million people annually, but OMS managed to eradicate the diseases through vaccination and in the last case was found in Somalia, in 1977. This was possible because smallpox transmits only from human to human. At the time of eradication, no effective cure was known against smallpox.
The first ever vaccine was created in 1798 by Edward Jenner and was against smallpox.
infects 2 million people annually and about 12 million diseased are found worldwide, mostly adult men. It is produced by a protozoa (Leishmania) that spreads through the bite of the sand flies (Phlebotomus).
The most severe type is “kala azar” (“black fever” in Hindu), which infects 0.5 million people, and incubation lasts some weeks. The parasite induces skin ulcers which extend all over the body and can produce obstructions or nasal hemorrhage.
It causes severe lesions on the legs and a temporary or definitive physical disability.
Kala azar swells the spleen and the liver and attacks the bony marrow and linph nodules. Without treatment, the parasite kills 75-95 % of the patients.
It is found mainly in Africa, China, India, Latin America, and outbreaks occur sometimes in Mexico and the US.
The best drug is Pentostam. Intravenous Amphotericin B is effective, like the Pendamidine, but there is no vaccine yet.
is found in 500 million people (!) and is caused by a protozoa spread by the female of the Anopheles mosquito. 300 million of these cases are severe. In the east African villages, children are bitten by the Anopheles mosquitoes carrying malaria 50-80 times a month.
It triggers fever, shivering, abundant sweating, articulation pains, severe headache, vomit and extreme weakness, so that the diseased cannot even cry.
Annually, 1.5 million people die of malaria (one million in Africa South of Sahara), a child every 30 seconds. About 120 million people died of malaria since 1914, and the disease is endemic in 101 countries, mainly tropical, in Africa, Asia and America.
It spreads during the rainy season, when the mosquitoes breed. Quinine extracted from the bark of the South American cinchona tree saved millions of malaria diseased. Many treatments have been developed (mefloquine, Halofantrine, Artemisia products) but none has a total effectiveness, as the parasite constantly mutates, and there is no vaccine.
5. Gonorrhea and syphilis
are triggered by two bacteria (Neisseria and Treponema pallida) and are transmitted sexually.
62 million people worldwide are affected, aged mainly 15 to 29 years, all over the planet, especially in urban areas and of low socioeconomic level.
In man, gonorrhea produces urinary incontinence, urethra pain, reddening, penis burning sensation and testicle inflammation. In women, it induces severe pain which reaches the trumps and uterus.
Syphilis induces ulcered lesion (syphilis chancre) at the entrance site. After that, it triggers skin eruptions, fever, hair loss, less severe hepatitis and gential condilloms, but if untreated, the lesions extend to the nervous system, leading to death.
The treatment consists in extremely powerful antibiotics (ceftriaxone, Cefixime, and others) which are also extremely costly.
affects 1 % of the planet’s population and can be produced by viruses or bacteria (like Aeromonas hydrophila).
It produces fever, shiver, sweating, cough with expectoration, muscle, head and thoracic pain, appetite loss, weakness.
This is the main cause of mortality in the world: it kills 3.5 million people each year. It attacks especially patients with severe immunodepression, those that follow chemotherapy, people who are older than 75, asthmatics, smokers, alcoholics, those with renal insufficiency and children under 2 years of age. It affects especially the poor countries.
Antibiotics work in the case of the bacteria. Therapy includes oxygen, liquids, and physiotherapy.
Patients with a simple pneumonia can cure in 2-3 weeks, but elders or those with debilitating diseases can die of respiratory or cardiorespiratory failure.
The vaccine trimetropin sulfamethoxazole is effective against the most frequent complications.
7. Sleeping sickness
is triggered by the Tripanosoma gambiense and T. rhodesiense, protozoans spread by the tse-tse fly (Glossina). The American variant, T cruzi, is spread by biting bugs and cause the disease called chagas.
The toxins of the parasites affect especially the central nervous system and the heart muscle. It manifests through fever, edemas, sleepiness, and meningitis.
It affects 60 million people, but only 4 million receive treatment, and it kills 150,000 people yearly.
It affects the livestock, being deadly or inducing low fertility, weight and productivity, with severe economical losses. It is found in the habitat of the tse-tse fly: over 10 million square km in 36 African countries. Chagas is found in certain areas of Central and South America.
DFMO, the effective drug, is already not produced. Currently, melarsoprol with arsenic are employed, fact that induces the death of up to 10 % of the patients. Vaccine exists only for the carrying livestock. There are also efforts to eliminate the flies in some areas.
is caused by the Koch bacterium. It is as old as the humankind. TBC was found even in mummies coming from the ancient Egypt and Peru. 2 million people die annually of tuberculosis. About 150 million people are estimated to have died of TBC since 1914.
One third of the people carry the Koch bacterium, which spreads through the air and affects all the body, especially the lungs. It induces prolonged coughing, fever, shivering, bloody expectoration, weight loss, sweating, tiresome, and glossy eyes.
It infects one third of the world population and each year another new 8 million cases appear. Each second a person dies of tuberculosis. It is more aggressive in women and persons between 15 and 45 years old. Mutant strains are resistant to almost all drugs and kill about 50 % of the patients.
It is worldwide spread, but its advance is rampant in Bangladesh, China, Indonesia, Philippines, India and Pakistan, with over half of the new cases.
TBC has a treatment, but it cannot be eradicated because of the emergence of multiresistant strains if the long and costly treatment, of over 6 months, is interrupted sooner than it should. 3-5 % of the new cases are coinfected with HIV.
The vaccine is effective in children, but useless in adults. Current employed drugs are isoniazid, ethambutol and Rifapentin.
is estimated to be found in 46-60 million people and it’s produced by the human immunodeficiency virus (HIV), spread through blood, semen, and vaginal fluids. Some say the virus is still in an early stage.
The symptoms come rather late and start with exhaustion and fever. After that, ganglion inflammation appears along with persistent diarrhea, pneumonia and weight loss. In the final stage, the patient’s state is profoundly altered.
Each minute, five new persons get infected with HIV, and the virus kills young people, found in their productive period. It has killed 25 million people since 1981 and about 3.3 million people with HIV die annually. 68 million people could die between 2000-2020. Africa has lost 20 % of its labor power. Lifespan in Sub-Saharian Africa is now of 47 years old; without the AIDS it would have been 62.
In developed world, 58 % of the new cases are drug addicts who share syringes and 33 % through unprotected sexual contacts, but in undeveloped countries is mainly through unprotected sex and blood transfusions.
28 million of the HIV infected are found in Africa, and 0.5 million in West Europe; 300,000 in Eastern Europe, 600,000 in Eastern Asia and Oceania; 2.6 million in America (mostly South America).
Antiretrovirals can improve the immunity but its price is too costly for about 95 % of the infected. Only 4 % of the patients in the developing countries receive treatments. This treatment can cost 6-18,000 Euro ($ 8-25,000) and the virus will get resistance to drugs if the treatment is interrupted.
In pregnant women, antiretrovirals during the second and third trimesters of the pregnancy can avoid the child’s infection.
There is no vaccine, and the combination of up to four different drugs is the main principle in stopping the disease. These drugs keep the blood lymphocytes at normal levels, maintaining the virus latent but without its deadly ability.
hit the world in 1918-1919 and killed over 30 million persons, soon after the First World War. Not even the bubonic plague had ever killed so rapidly so many persons. Typhus outbreaks use to accompany war conflicts. A huge typhus pandemic outbroke during the First World War in the eastern Europe. Since 1914, over 20 million people died of typhus.