Category Archives: Guest Blogger

A possible new HIV vaccine target?

Contributed by guest blogger: Lydia Mendoza ’11

In 2009, it was estimated that 33.3 million people in the world were living with HIV/AIDS. Since the discovery of HIV, more than two decades ago, money has poured into research in the hopes that an effective vaccine might be developed. As of yet a vaccine remains elusive. One reason why it is so difficult to create a vaccine is because HIV is highly mutable and genetically diverse subtypes, or clades, have evolved. A vaccine needs to be able to offer protection from a range of HIV clades.

Normally viral vaccines are based upon neutralizing antibodies, which prevent infection of the host cell. The first attempts to develop neutralizing antibodies against HIV targeted gp120, which is known to play a role in HIV’s ability to enter and infect CD4 t-cells. These attempts have not been successful as of yet because of the gene’s high rate of mutations. However a recent paper has shown that the V3 loop of gp120 is a potential vaccine target.

The strand of protein known as the V3 loop was never thought to be an attractive vaccine target because it is not highly conserved. However, it appears to have conserved structural elements that are involved in interactions with coreceptors. To study whether V3 was a viable vaccine target, a human monoclonal antibody, HGN194 was used. HGN194 was isolated from memory B cells of a person infected with HIV-1 clade AG circulating recombianant form (CRF). HGN194 targets the V3 loop and has been previously shown to neutralize a broad range of neutralization-sensitive and resistant strains of HIV.

The study evaluated whether HGN194 was able to protect rhesus monkeys from an HIV model system. One group of monkeys was injected with HGN194 then they were challenged with a high dose of a clade C SHIV, which is a chimeric simian-human imunodeficiency virus encoding HIV envelope genes in a SIV backbone. The second group of monkeys was also given a high dose of SHIV but was not given the HGN194. The monkeys given the antibody were protected from SHIV infection, and those not given the antibody were infected. The researchers concluded that HGN194, isolated from an HIV-positive individual harboring a clade AG CFR, was able to confer complete cross-clade protection against clade C SHIV.

The antibody apparently latches onto the virus’s V3 loop and prevents the virus from invading cells. This does not mean that this antibody treatment technique is a vaccine for HIV. It does not create long-term protection because the antibodies do not remain active in the body for very long. This is only a first step. A vaccine target has been identified but now scientists must create an antigen that induces formation of an antibody similar in structure to HGN194. There is a lot of work left to be done but this finding hopefully brings researchers much closer to the development of a vaccine.


The strangest family reunions

Contributed by guest blogger: Amelia McKitterick ’11

Next time you are sick from a viral infection, you should ask yourself if you’re just hosting a visit from distant relatives. Although “relative” might not seem like the most appropriate term for a virus, there has been evidence of a history viral influences and insertions into animal genomes, including that of humans!

A crucial step in the replication of RNA retroviruses is the integration of the viral genome into the host genome. Fragments of a viral genome in the genome of a non-viral cell are called endogenous viral elements (EVEs), and they can either be phased-out of the host genome or be passed on to become fixed within a population. A recent study examined genomes of a variety of mammals, birds, and insects for EVEs with matching amino acid sequences to extant, non RNA retroviruses. The genomes of 44 animals were converted into amino acid sequences and checked via tBLASTn (a BLAST that matches amino acid sequences with nucleotide sequences) for alignment with a library of currently known mammalian viruses with genomes larger than 100 kb in length. Matches were found to viruses with all types of RNA genomes (ss/ds, +/-, segmented, un-segmented) in all three of the major phyla tested, matches to DNA genomes (ss/ds, rt) were only found in mammals and birds, and even unclassifiable viral proteins were found in mammals that could represent extinct or undiscovered lineages.

But what is the use of all this new information? First, the data can be used to determine the minimum evolutionary divergence dates of different viral families based on host divergence dates. This study of paleovirology estimated the minimum ages of virus fossils Parvo-, Circo-, Filo- and Bornaviridae within the mammalian samples and found the oldest (Borna-) to be about 93 million years old, where it was originally infecting the distant relatives of the Afrotheria clade (Elephants, hyrax, tenrec, etc. For reference, the common ancestor of the primates evolved about 85 million years ago). A second use of the data is to illustrate the variety of viruses, and to give a better indication of the types of viruses that infect different hosts. The presence of the EVEs in a host genome can provide new insight about the replication process of non-reverse transcription viruses, and show patterns of host vulnerability. Similarly, new viruses, such as the unclassifiable EVE in mammals, could lead to new routes of investigation into the types of viruses and cures to infections.


A different alphabet, a different treatment?

Contributed by Guest Blogger: Sean Koerner ’11

It’s easy to think of viruses as alien or lifeless – after all, they can’t reproduce on their own, eat anything, or even move around without assistance. However, viruses have evolved to use the same toolbox that human cells use, right down to the way their genes and proteins are encoded. One of the most problematic viruses for humans, HIV, works by putting its own information into our cells’ genomes, turning host cells into viral factories. This information is formed from two types of alphabets: strung-together sequences of deoxyribonucleotides, which exist intracellularly as deoxyribonucleotide triphosphate (dNTP) monomers in our own cells and ribonucletides, which form the HIV genome as well as existing independently as ribonucleotide triphosphate (rNTP) monomers within our own cells. In order to infect our cells, HIV uses a protein known as reverse transcriptase to generate the DNA that our cells are used to reading from the viral RNA genome. This reverse transcription of RNA to DNA has long been a target of anti-HIV drugs, since without this step, HIV cannot successfully infect our cells.

Recently, a team at the University of Rochester discovered a previously unknown characteristic of this process. Two of the cells most commonly infected by HIV, CD4+ lymphocytes and macrophages, displayed different levels of dNTPs and rNTPs after being infected by HIV, with the lymphocytes containing much less rNTPs and more dNTPs than the macrophages. After a biochemical analysis of the cells, the research team discovered that HIV’s reverse transcriptase is capable of using cellular rNTPs to generate RNA based upon the HIV genome, which is then reverse transcribed into cellular DNA while in the macrophage environment. This allows HIV to use the higher concentrations of rNTPs in macrophages to continue replicating efficiently, despite the relative dearth of dNTPs as compared to lymphocytes. Since HIV uses one method (dNTPs) in lymphocytes and one method (rNTPs) in macrophages, it may be possible to target HIV replication in macrophages specifically. Why care about the difference between the two cell types? Well, macrophages travel the body much more rapidly than lymphocytes; if we can stop HIV infecting them, we may be able to slow the progression of HIV infection throughout the body.

How could we do that? In short, by targeting the synthesis of rNTP strands with new drugs. Although we would likely experience side effects, they could be negligible compared with the repression of HIV. The research team at Rochester have already demonstrated that rNTP string inhibitors slow HIV’s infection of macrophages, so specific drugs targeted for this process might be able to halt it altogether.


Chicken Anemia Virus and its Similarities to Human Anelloviruses

Contributed by Guest Blogger: Maggie Rasnake ’11

When a virus is not known to be associated with any disease, it is called an orphan virus. Human anelloviruses, like torque teno virus (TTV) and torque teno mini virus (TTMV), are orphan viruses because they do not have known symptoms. TTV was first discovered in a patient with liver disease. However, no definite link between liver disease and the virus has been shown. Anelloviruses are genetically similar to an avian virus called chicken anemia virus (or CAV). CAV has had a large, economic impact on the poultry industry. Unlike TTV, it is known to have symptoms, but it can have a long lag-time between infection and the development of disease.

Both CAV and TTV have similar, single-stranded, circular DNA and have highly variable sections of the genome. It is believed that they evolved from a plant virus. Researchers realized that much of what they learned about CAV could be applied to TTV and vice versa. For example, when they realized that TTV had more than just three proteins encoded by its three open reading frames, they found that the same was true for CAV. When CAV was found to replicate in the bone marrow, it was discovered that a great deal of TTV replication occurs in the bone marrow as well.

CAV is associated with developmental problems for fetuses and young chickens. The virus is less understood in adult chickens, but when chickens have CAV, they are much more likely to suffer from other diseases and have higher mortality rates. Similarly, in infected humans, the viral load of TTV is higher when the individual has other infections. In addition to liver disease, levels of TTV tend to be higher in those with respiratory infections, kidney disease, HPV, and certain cancers, among others. TTV may enhance the pathogenic effects of other pathogens. High levels of TTV are found in individuals with HIV, but it is not known if TTV simply reflects the immune system’s status or if it contributes to the damage. An effective medium for studying TTV has not yet been established. The authors suggest that the virus might be better studied in a novel primate cell line transformed by an oncogenic virus.


Eat Your Vaccines

Contributed by guest blogger: Nicole Engelhardt ’11

Usually when you get a vaccine it means you get a needle and a bandage. Not only that, but you get an attenuated virus. These weakened virus particles are strikingly similar to viable ones; they even infect cells. Because of their weakened state, they infect slower than natural virus particles, giving the body time to react. However, people who have weakened immune systems can still exhibit symptoms as if they were infected by the natural virus.

But a new tool may make this issue obsolete. What really matters when it comes to a vaccine is the shape of the particle, not the contents. The shape is recognized by B-cells in the body which then reproduce creating antibodies that attack all of the virus particles. However, these B-cells are very specific and very picky. Normally, it makes sense to use a weakened virus because it has the exact same shape as a normal virus and your B-cells will react to the vaccine as if it were the real thing. Is there any way, then, to produce the exact shape of the virus and therefore the correct antibodies without having the harmful side effects?

This paper explores the rotavirus particle which is the leading cause of gastroenteritis in the world. In some parts of the world, gastroenteritis can be deadly for many children. As it happens, the shape of the rotavirus particle can be mimicked almost exactly in plants. The shape of this virus is a capsid made out of proteins. First, the authors take the genes that code for the capsid proteins and insert it into the genome of the plants. Then the plants express the viral genes, creating the virus capsid proteins inside the cells of the plants. More incredible than that, these proteins self-assemble into the exact shape of the rotavirus capsid. Now you have a plant containing just the shell of the virus!

The experiments are still in their early stages, but when mice were fed these plants, the authors found they were producing the same antibodies that are produced when mice are actually infected with rotavirus. This bodes well for future research in humans. Once the antibodies are created, the severity of future infections is greatly decreased. If these transgenic plants do work, it could mean a safer and perhaps more affordable form of the vaccine that could help people the world over fight rotavirus before it can infect.


The Relationship Between Diabetes and Enteroviruses

Contributed by Guest Blogger: Charlie Gray ‘11

Enteroviruses are a genus of positive sense, single-stranded RNA viruses which include poliovirus, coxsackie A & B, echovirus, and enterovirus. These viruses can cause a variety of symptoms ranging from the common cold and conjunctivitis to paralytic poliomyelitis. Researchers have also found an association between enteroviruses and type 1 diabetes, a disease whose incidence has increased over the past 25 years at an annual rate of 3%, a rate that cannot be explained simply by genetics.

In a recently published paper, Wing-Chi G Yeung and his colleagues conduct a systematic review of controlled studies that use molecular virological methods in an effort to compile what is currently known about the association between enteroviruses and type 1 diabetes, and to aggregate their results. Their meta-analysis included 34 papers, 30 of which used reverse transcriptase PCR or in situ hybridization to detect the enterovirus RNA; the other four used immunostaining for the enterovirus capsid protein, vp1, on autopsy pancreas specimens. Although the studies varied in age distribution, most investigated children and adolescents (i.e. less than 16).

Yeung and his colleagues found a strong association between enterovirus infection and diabetes, with a 9 fold increase in the risk of infection in diabetic individuals. They conclude that their meta-analysis of these previous observational studies do provide support to the growing collection of findings that individuals with type 1 diabetes have increased odds of suffering from an enterovirus infection.

Despite Yeung et al.’s findings, there was quite a bit of variation in the designs and methods used in the various studies that the authors analyzed. Only 10 of the 34 studies matched for three or more potential confounding factors such as age, genetic risk, geographical location and sampling time. In addition, the studies varied greatly in the site selection from which they collected samples (e.g., serum, stool, throat swabs). Enteroviruses invade cells and replicate at mucosal surfaces; therefore, detection rates could be significantly higher in samples that were obtained from the gastrointestinal tract.

Although this paper does provide evidence for a diabetes-enterovirus link, it does leave several questions for future research. It is unclear how strong the association between enterovirus infection and diabetes is, and if the other factors such as geographic location and genetics may influence the observation of enterovirus infection and diabetes. For example, previous studies have examined varying HLA (a gene encoding an important immune system protein) genotypes and how certain genotypes can modify the association between enterovirus infection and diabetes; however, those results have provided conflicting evidence. Therefore, further study is needed to determine how these confounding factors affect one another and the enterovirus-diabetes link.


The Role of Social Networks in H1N1 Transmission Within a School

Contributed by Guest Blogger: Aaron Grober ’11

The H1N1 subtype of the Influenza type A virus, known colloquially as “swine flu,” was the most common cause of human influenza infection in 2009, and remained a major concern in sparking a pandemic throughout the 2009/2010 flu season.

This recent paper examines the role of grade, class, and social network in transmission of this virus in a school setting. Taking a closer look at the actual transmission pattern of this novel subtype of influenza is critical in developing models to better predict and combat pandemic spread. In the case of this school, closure due to outbreak did not significantly affect transmission among students, indicating that it may have occurred too late to be effective, stressing the importance of more exact models. The study encompassed 370 students from 295 households, surrounding an H1N1 pandemic that occurred in a Pennsylvania elementary school in April and May 2009.

The researchers found that the structuring of the school into grades and classes significantly affected the probability of transmission: 3.5% between students within a class, five times less than that between students of the same grade but different class, and five times less than that between students of different grades.

The researchers took an in-depth look at fourth-graders. They note that children are four times more likely to play with members of the same sex, and found that this behavior had a significant impact on disease transmission; the onset of epidemic transmission occurred among boys significantly before that of female classmates. In addition, they found no significant difference between recorded playmate transmission rates, and the expected proportion for if being a playmate was not a risk factor. The researchers used class seating charts to determine if proximity to an infected individual affects the risk of transmission; as it turns out, they found that sitting next to an infected individual did not significantly affect one’s risk.

In addition to school structure, the researchers looked at spread within households. The probability of a child to adult transmission within a household depended significantly on the household size, where probability of spreading the disease is much lower in larger households than smaller ones. The predominant means of adult infection was from outside the home.

These unique findings shed light on the extremely complex transmission pattern within structured populations. The biggest factors for transmission within school are grade and class, but not seating arrangement, sex, but not playmate transmission. A number of obvious questions remain: Why does sharing a class, but not a desk-space affect transmission? Why is one more likely to transmit the disease in a smaller household than a larger one? This study is an extremely insightful epidemiological tool to help explain transmission, but our knowledge of how this virus spreads remains incomplete; it seems that the flu is far more complex than we imagined.


Feeling tired all the time? You might have a virus.

Update (Janyary 2012): Two studies identifying XMRV in CFS patients have been retracted, including the original paper that proposed the association. The current, best supported evidence, in this area suggests that the association was actually due to contamination. There appears to be strong scientific agreement that CFS is not related to infection with this virus.

Contributed by Guest Blogger: Nicole Krenitsky ’11

Patients with Chronic Fatigue Syndrome (CFS) perked up when a paper published in Science in 2009 linked the symptom-defined illness to xenotropic murine leukemia virus-related virus (XMRV). XMRV, also connected to prostate cancer, is positive sense, single-stranded RNA retrovirus of the class murine leukemia viruses (MLV). Four subsequent studies failed to find any MLV-related viruses in CFS patients or controls. Then in 2010, a paper published in PNAS reinvigorated the debate. The study did not specifically find XMRV but did find MLV-related viruses in the blood cells of CFS patients tested. Yet one month later, the CDC published report, stating that they had not found any MLV-related viruses in their own study of CFS patients.

Reasons for the inconsistent results are presently unknown. One hypothesis is that the PCR could have picked up mouse DNA or mouse viruses, contaminating the tests and producing false positives. Another involves the samples of participants; CFS is diagnosed solely based on symptoms and clinical case definitions such as the one published by the CDC do not differentiate well between CFS and depression, resulting in overdiagnosis. A study conducted by Ian Lipkin is underway and seeks to standardize sampling and analysis methods and use a larger sample size to settle the controversy.

Relating CFS to a virus has far-reaching consequences for patients and for public health. Antiretrovirals used to treat HIV have been shown to inhibit XMRV replication in vitro and some CFS patients have already begun ART following the 2009 Science publication. The AABB and the American Red Cross, erring on the side of caution, have banned patients with CFS from donating blood erring on the side of caution. If CFS is caused by MLV-related viruses, the blood supply would be tainted the syndrome passed to transfusion recipients.

One million Americans are affected by CFS and experience sleep disorders, cognitive difficulties, chronic muscle pain and headaches. Many dismiss the disorder as psychosomatic and doubt its legitimacy as an illness. In addition to diagnostic testing and finding clinical treatment or a cure for CFS, a link to a virus would give CFS scientific credibility. Mary Schweitzer, historian and CFS sufferer explains, “Patients are hopeful that now the disease itself might be treated seriously, that they’ll be treated seriously, and that there might be some solution.”


New Vaccine Protects Against Ebola Virus

Contributed by Guest Blogger: S. Goldberg ’14

Ebola Virus (EBOV) is a fairly new infection of the Filoviridae family, that causes Ebola Hemorrhagic Fever, or EHF. This infection can often be severe or fatal in humans and primates. Because it would be difficult to create a vaccine against all four different virus species of Ebola, scientists came up with a plan to develop a vaccine protective against a single species of the infection. An experiment was designed to test to see if a “prime-boost” strategy would work, with a vaccine protecting against one Ebola Virus species and protecting a different species at the same time. In the process of doing this experiment, it was found that the vaccine developed to protect primates against the two most lethal Ebola Virus species also protected against the newer Ebola virus species that was founded in 2007. The prime-boost vaccination provides immunity against newly emerging EBOV species and shows cross-protection against EBOV infection. In this strategy, the “prime” is a DNA vaccine that has a small amount of genetic material with surface proteins of the Zaire Ebola virus species and the Sudan Ebola virus, the two most lethal species of EBOV. The “boost” is made of a weak cold virus that delivers the Zaire EBOV surface protein. The experiment, conducted and overseen by the National Institute of Allergy and Infectious Diseases and the US Army Medical, gathered eight 3 to 5 year old cynomolgus monkeys as their test subjects, to see if such a vaccine actually protected against the two older Ebola virus species and the newer strain. Each of the monkeys were given the immunization and then transferred to a laboratory where they were exposed to the EBOV infection. The monkeys stayed their for the duration of the experiment. Using a blood analyzer, liver enzyme levels were examined on “days 0, 3, 6, 10, 14, 21 and 32”. During this test, samples of T-cell intracellular cytokines were taken. CD8+ T-cells were stained with antibodies, against intracellular cytokines. This technique allows for the frequency of antigen-specific T-cells to be determined. The production of cytokines plays an important role in the immune response of the body. After isolating the RNA of each subject, each of the monkeys given a vaccine that contained Zaire EBOV and Sudan EBOV glycoprotein (GP). After the GP was exposed within each of the bodies, the subjects developed “robust antigen-specific…immune responses against the GP from [Zaire EBOV] as well as cellular immunity against lethal…[Bundibugyo EBOV]”. After concluding this experiment, scientists have learned that current vaccines that can bring about T-cell immunity will have a greater possibility of “protecting against other [new] pathogenic EBOV species”.
If we have the ability to protect against new and emerging EBOV species, does that mean that, in the long-run, mutation of the virus will stop? Will existence of any EBOV species disappear? If it disappears, could it reappear? Could similar experiments be done to discover if a other currently used vaccines, aside those that display T-cell immune responses, are protecting against other unknown or new viral strains?


New Treatment Found for Chronic Hepatitis B Virus

Contributed by Guest Blogger: S. Bhutani ’14

Chronic Hepatitis B virus (HBV) is a common infectious disease. HBV infects hepatocytes, which are liver cells, thereby impairing liver function and leading to disease such as liver cancer. In chronic HBV the responses from the CD8 cytotoxic T-cell and CD4 helper T-cell are not substantial enough because high amounts of HBV impair T-cell immunity. Thus, ideal anti-viral treatments would need to reduce the amount of virus. In the past decade, the introduction of nucleoside and nucleotide analogs, compounds that look similar to nucleotides and deceive the virus into thinking it is being replicated, has improved treatment for HBV. However, the prominent nucleoside analog, lamivudine, that inhibits HBV replication, is no longer as effective because the virus has developed mutations that resist the drug. One new nucleotide analog, called adefovir dipivoxil, has been tested on chronic HBV patients in China.
In China 22 patients were tested along with 20 healthy controls. The patients were treated with adefovir dipivoxil once daily for 10 weeks. The presence of cytokines producing certain T-helper cells was measured, as was the amount of HBV DNA using biochemical markers. Before adefovir dipivoxil, the cytokines producing helper and killer T-cells were lower in the patients than the healthy individuals. There were two patients with HBV mutations, one which was lamivudine resistant and one which was adefovir dipivoxil resistant. Adefovir dipivoxil treatment resulted in an increase of Th1 and Th2 cytokines that produce CD4 T-cells in all patients except for the one with the adefovir dipivoxil resistant mutation, proving that this new drug can combat lamivudine resistant HBV mutations. The treated patients’ levels of cytokines peaked and then dropped and stayed at the cytokine levels of the healthy individuals. There was an inverse correlation between the amount of HBV DNA and cytokine levels; after treatment as cytokine levels increased, HBV DNA decreased.
Thus, this study suggests that adefovir dipivoxil inhibits HBV DNA polymerase thereby reducing the amount HBV and restoring T-cell immunity. However, it should be noted that even after the recent development of the drug, HBV mutations were still found. Thus will there ever be development of a treatment for which there no resistant mutations have already evolved?