Category Archives: Guest Blogger

Creating Synthetic HIV Vaccines

Contributed by Guest Blogger: A. Lee ’14

HIV is particularly virulent due to its specific attack of host immune cells and disruption of their normal function. The human body needs helper T-lymphocytes (HTL), which coordinate and activate other immune cells, and cytotoxic T-lymphocytes (CTL), which attack infected cells, to work cooperatively to defeat illness. HIV attacks HTL and through its high sequence mutation rate evades the body’s attempts to identify a parts of it for counterattack, called epitopes; these constant, minute changes in the virus also makes vaccine development difficult. However, recent technological advances have allowed immunologists to circumvent this problem through study of HIV’s amino acid sequence, or its structural makeup.
Researchers have identified key epitopes of major HIV subtypes, recognizable by HTL and CTL, and combined them into two vaccines, a synthetic protein structure to activate HTL (called EP-1043) and a plasmid (DNA segment, EP HIV-1090) to activate CTL. EP-1043 was created by cutting the DNA sequence of the 18 epitopes into overlapping sequences, fusing that with insect and viral sequences to ensure viability in a bacterium, and using this sequence in a non-deadly virus to force a bacteria to create the protein. The EP-1090 DNA sequence was created using a similar process of combining epitopes into overlapping sequences and replicating them using a process called PCR (no similar process exists for replicating proteins). Importantly, EP-1043’s protein epitopes are joined by weak bonds, meant to break and spread the epitopes through the body. Because the protein aggregates (becomes useless) at blood pH, it is packaged in aluminum hydroxide (Alhydrogel) and aluminum phosphate gels, which dissolve later.
Effectiveness of the virus was measured 39-42 days after infection by measuring cytokine (cytokines are secretions of infected cells causing immune reaction) and by measuring reproduction of splenocytes (spleen immune cells). Though EP-1090 was ineffective, EP-1043 was significantly effective in causing immune. Despite the low toxicology of the vaccine, and the fact that a true vaccine for HIV would require CTL and HTL epitope response from singular cells, this is an important step towards combating HIV.
One wonders, then, what more complex methods can be used to amalgamate epitopes for vaccines, and what method immunologists will use to create true HIV vaccines, if at all possible. This method can be used for other, less complex viruses, but does this relatively non-specific, general epitope flood lessen the necessary specific response? Can the body handle such a large, sudden appearance of viral material?


Cross-Species Transmission in Rabies

Contributed by Guest Blogger: D. Patel ’14

Deadly human diseases including HIV Aids, swine flu and rabies are infectious diseases where the viruses have jumped from one animal species into another and now infect humans too. This is a phenomenon known as cross-species transmission (CST). Understanding this process is the key to predicting and preventing future outbreaks.
The scientists who researched CST and wrote this paper made a groundbreaking discovery into how viruses jump from host to host. They used and thought of rabies as an ideal system because it occurs across the country, affects many different host species, and is known to mutate frequently. Although cases of rabies in humans are rare in the U.S., bats are a common source of infection. Hence, the study was based on and narrowed down to CST events among different bat species.
To determine the rate of CST, a large dataset containing hundreds of rabies viruses from 23 North American bat species was used. Population genetics tools were used to quantify how many CST events were expected to occur from any infected individual and the cases were verified by genotyping both the viruses and the bats.
The study showed that depending on the species involved, a single infected bat may infect between 0 and 1.9 members of a different species; and that, on average, CST occurs only once for every 72.8 transmissions within the same species. This means that the majority of viruses from cross-species infections were tightly nested among genetically similar bat species.
It is a long-held belief that CST depends on virus mutation and contact of the host with other species. However, this study showed that CST may have more to do with host similarity. The similarity in the defenses of closely related species may favor virus exchange by making it easier for natural selection to favor a virus’ ability to infect new hosts.
Whether other factors (like evolution of viruses) are enough to overcome the genetic differences between hosts remains questionable. However, the basic knowledge gained through the study is key to developing new intervention strategies for diseases that can jump from wildlife to humans.


Redefining the HPV-32 Detection Gold Standard

Contributed by Guest Blogger: R. Hendricks ’13

A recent study focuses on HPV-32, which is frequently associated with focal-epithelial-hyperplasia (FEH), which is a wart-like growth in the mucous tissues of the mouth. Detection of HPV-32 is currently labor-intensive and insensitive, so this work was focussed on testing an experimental polymerase chain reaction (PCR) assay, or measurement of the virus in a sample, to determine if it was more sensitive and user-friendly than the current gold standard method (MY09/11 amplification and dot blot hybridization).
The experimental assay was specific for the HPV-32 L1 gene, so the experimenters used samples of the HPV-32 gene from HPV-positive subjects and tested sensitivity of the current dot-blot assay by applying it to the sample and seeing how many copies of the gene it could detect and amplify. They then did the same procedure with the experimental assay, which correctly identified many more genes as HPV-32 positive. Specifically, the dot-blot assay detected HPV-32 in 24 oral samples. All but one were also identified by the HPV-32 L1 PCR, which identified an additional 78 samples. Reproducibility was also assessed, by retesting 111 samples, 57 of which were HPV-32-positive. The researchers found that 94.6% of the samples were reproducible.
The HPV-32 specific PCR system targeting the L1 gene produced significantly greater sensitivity in identifying HPV-32. It is also highly reproducible and less labor-intensive, and is therefore the new gold standard.
Follow-up experiments, such as one that targeted a different gene of HPV-32 (the E6/E7 region) were carried out to ensure that the increased sensitivity was a result of the robustness of the experimental assay. A potential next step in this research could be to target other specific genes with a similar PCR assay, to see if the robustness will remain.