Monthly Archives: March 2011

Antiviral Drugs, Guest Blogger, Molecular Virology

A different alphabet, a different treatment?

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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.

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Epidemics, Uncategorized

Hey, I wonder what’s in bat poop?

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I know you were thinking the same thing! Bats are suspected reservoirs for several zoonotic viruses that can cause significant disease in humans or other animals. These include the dreaded Ebola virus, Nipah virus (which causes outbreaks of encephalitis in South East Asia), Hendravirus (which causes disease in horses) and several others. So knowing what viruses are carried by bats will be important in understanding emerging zoonoses.

Several studies have identified a diverse array of viruses in bats, but using next-generation sequencing it is now possible to investigate the population of viruses carried in bats to a much deeper level. In a study published last summer, guano from bats in California and Texas was collected by placing plastic sheets below the bat roosts. The individual roosts were occupied by as many as four different bat species, so the guano collected was a mix from the different inhabitants. To isolate viral DNA and RNA, the samples were filtered to remove cells then treated with nucleases to destroy any free DNA or RNA, leaving only encapsidated viral genetic material.

In the sequenced “virome” or population of viruses in the samples, only 51-39% of the sequences(depending on collection site) had matches to genbank sequences. So once again, viromic sequencing shows us how little we know about the viral world. Of those sequences that matched known sequences, most were insect and plant viruses. The bats are insectivores and the insects are herbivores, so you can see the viral populations from each link in the food chain. Only a very small proportion of the virome was of bacteriophage origin, much less than other viromic studies in humans and horses, although its not clear why there would be such a difference. Among mammalian viruses, which made up less thatn 10% of the sequences, there were adenoviruses, coronaviruses, parvoviruses, circoviruses, astrovirsues, picornaviruses and even poxviruses. Most of these sequences only matched less than 60% to known mammalian viruses however, so its unlikely that they pose a zoonotic threat.

As researchers continue to sequence viral populations, we keep seeing mostly novel sequences, something that has decreased in bacterial and eukaryotic sequencing. That tells us we have a lot more sequencing to do if we want to understand global viral diversity. In bats however, the major question is not so much about the diversity but the threat of zoonoses. It will be interesting to see the guanome of bats in areas where zoonoses are a real problem, and I wonder if this will be a technique useful to monitor the threat of emergent diseases as the cost of high throughput sequencing continues to drop.

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Epidemics, Evolution, Immunology

Virus and Parasite Unite

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Contributed by Guest Blogger: Joseph Zaino ‘11

Recent research has found a unique relationship between the intracellular parasite, Leishmania, and it’s corresponding Leishmania RNA virus-1 (LRV1). Ives et. al. concluded that Leishmania parasites, in the presences of LRV1, suppressed the host immune response and strengthened the pathogen’s persistence. Leishmania infects the human immune system by attacking macrophages. The parasite causes the infection known as leishmaniasis, which is typically transmitted by sand files. This is a serious infection, affecting an estimated 12 million people in the Mediterranean basin, Africa, the Middle East, Asia, Central and South America. The strain of parasite investigated by this study was mucocutaneous leishmaniasis (MCL). MCL destroys the soft tissues of the face and nasopharyngeal regions, as well as damages host immune responses.

Leishmania parasites are dependent on proinflammatory protein mediators called Toll-like receptors (TLRs). TLRs are found in intracellular vesicles of the macrophage- presumably the same vesicles that host Leishmania. Ives et. al. confirmed that TLR3-TRIF dependent pathways are essential for macrophage infection by Leishmania. The unusual part is that TLRs usually help the mammalian immune system to eliminate pathogens. Specifically, TLR-3 recognizes the double stranded RNA of many viruses that are released from dead parasites, unable to survive within their host. Observations found that between virally infected and non-virally infected Leishmania, the virally infected ones were more likely to successfully infect a host. Similarly, metastasizing parasites had greater levels of the LRVI virus than non-metastasizing parasites. The authors verified this finding by treating macrophages with purified LRVI, and observing the same phenotypic infection as the viral-infected Leishmania. Further models concluded that when TLR3 is deleted from macrophages, parasitic persistence was diminished.

This apparent mutualism seems to benefit both Leishmania and the virus by allowing a more successful rate of host infection. Many Leishmania species have lost RNAi interference pathways, allowing viruses to inhibit and replicate within them. In this case, the virally infected parasite is more persistent against macrophages, and more damaging to the mammalian immune system. Thus, it is advantageous for the parasite to coexist with the LRV1 virus. If severe MCL infections are contingent on LRV1 for infection, then future research can perhaps focus on this relationship in order to better understand and cure leishmaniasis.

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Epidemics, Guest Blogger

Chicken Anemia Virus and its Similarities to Human Anelloviruses

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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.

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