Ebola Virus Primer

Ebola Virus is in the news again. The latest Ebola outbreak in Africa has killed more than 670 people including a prominent Liberian doctor and two American doctors. World Health Organization (WHO) calls the latest outbreak the largest recorded outbreak to date.  Ebola virus always conjures up in my mind images of an inevitable and horrible death by bleeding out of every orifice. Despite being discovered in 1976, even before AIDS and HIV, I realized that I didn’t know very much about the virus or how it worked, other than the occasional blurbs that appear in the news at the time of an outbreak. So I decided to look into it. It’s not that the basic information is difficult to find—my primary sources were the WHO and CDC fact sheets about Ebola Hemorrhagic Fever, and of course, Wikipedia. I did, however, also look in the scientific literature for some review articles and to see what research is currently going on in the field. For this article, though, I will just present the basic facts about Ebola Virus and the disease it causes, and other information you might be interested in, such as how contagious is it, how lethal is it, and how do you treat it. I will follow up later with more scientific details for those who want to learn more.


Ebola Virus  is endemic to Central and West Africa near tropical rainforest areas. It is initially spread to humans by contact with infected animals, most likely fruit bats, which are thought to be the most likely reservoir.


According to information published by The WHO and CDC, Ebola causes an acute and rapidly progressing hemorrhagic fever. The disease often begins with the sudden onset of fever, intense weakness, muscle pain, headache and sore throat. This is followed by vomiting, diarrhea, rash, impaired kidney and liver function, and in some cases, both internal and external bleeding (WHO). The incubation period, the time between infection and onset of symptoms, can be anywhere from 2 to 21 days, with an average of about 14 days. Disease progression and death are rapid, thus somewhat limiting the spread of an outbreak.

What is the treatment?

There is currently no treatment for Ebola hemorrhagic fever other than supportive therapy such as maintaining fluids and electrolytes. There are no drugs or anti-viral treatments.

How lethal is Ebola?

The mortality rate of Ebola hemorrhagic fever is 50-90%.

How contagious is it?

Ebola is highly contagious during outbreaks. It is spread by direct contact with  bodily fluids of an infected person. There is no evidence to date for natural spread of Ebola by an airborne route, but airborne transmission cannot be ruled out (4). People are infectious as long as their blood and secretions contain the virus. Ebola virus was isolated from semen 61 days after onset of illness in a man who was infected in a laboratory. (WHO).

Is there a vaccine?

There is no vaccine available yet, but work is in progress.



Ebola Virus is a member of the Filovirus family, along with the Marburg and Cueva viruses. There are five known species of Ebola: Zaire ebolavirus (EBOV), Sudan ebolavirus (SUDV), Reston ebolavirus (RESTV), Côte d’Ivoire ebolavirus (TAFV), and Bundibugyo ebolavirus (BDBV). The Reston virus was isolated from cynomolgous monkeys imported from the Philippines. The Reston virus infects humans, but does not cause disease—so far. (CDC)


The genome of Ebola Virus is a 19 Kb (-) sense RNA, most similar  in genome size and organization to mumps, measles, and Respiratory Syncytial Viruses (RSV). The (-) or negative sense of the RNA strand means the virus genome must be transcribed into a (+) sense strand which then serves as messenger RNA for the production of virus structural proteins. The virus codes for, and carries with its virions, an RNA-dependent RNA polymerase to carry out the transcription and replication process.


Photo credit: "Ebola virus virion" by CDC/Cynthia Goldsmith - Public Health Image Library, #10816 This media comes  from the Centers for Disease Control and Prevention's Public Health Image Library (PHIL).
Photo credit: “Ebola virus virion” by CDC/Cynthia Goldsmith – Public Health Image Library, #10816 This media comes
from the Centers for Disease Control and Prevention’s Public Health Image Library (PHIL).

Ebola Viruses form long filamentous virions 80 nm in diameter, and  are highly variable in length, from 500-1400 nm. Ebola virions are usually seen with loops or knots at one end by electron microscopy (see photo).

Components of the Virus Particle (Virion)

Ebola virions consist of seven structural proteins: the nucleocapsid protein (NP), a polymerase co-factor VP35, a transcriptional activator VP30, two matrix proteins, VP40 and VP24, the envelope protein GP, and the RNA- dependent RNA polymerase L. The helical nucleocapsid core consists of the genomic (-) RNA surrounded by a sheath of nucleoproteins (NP), and is associated with the RNA-dependent RNA polymerase (L), with the other proteins present in the virion cores. The virions are surrounded by a lipid membrane derived from the host cell membrane as the particles bud from the cell. The membrane contains the envelope proteins GP which allow the newly formed viruses to recognize, bind to, and infect their target cells.

I will follow up later with more on the molecular biology of the virus and the mechanisms of pathogenesis, in particular, the interaction between the virus and the immune system.


  1. Ebola Virus Disease. WHO Fact Sheet. http://www.who.int/mediacentre/factsheets/fs103/en/
  2. Ebola Hemorrhagic Fever. CDC Fact Page.   http://www.cdc.gov/vhf/ebola/
  3. Ebola Virus Disease. Wikipedia:  http://en.wikipedia.org/wiki/Ebola_virus_disease
  4. Zumbrun EE, Abdeltawab NF, Bloomfield HA, Chance TB, Nichols DK, Harrison PE, Kotb M, and Nalca A. 2012. Development of a Murine Model for Aerosolized Ebolavirus Infection Using a Panel of Recombinant Inbred Mice.
  5. Viruses 4: 3468-3493.
  6. Sullivan N, Yang ZY, and Nabel GJ. 2003. Ebola Virus Pathogenesis: Implications for Vaccines and Therapies. J. Virol 77: 9733-9737.

Role of Nef in HIV Pathogenesis–Revisited

HIV transmission-2

I came across a review article in Nature Reviews Microbiology this morning, describing recent advances in our understanding of how HIV is spread. The article also allowed me to revisit the role of the Nef gene/protein in HIV pathogenesis. I worked on HIV Nef in the early 1990s in the laboratory of Dr. J. Victor Garcia at St. Jude Children’s Research Hospital.

The name Nef is an abbreviation of “negative factor” It was so named because early experiments suggested that the protein had a negative effect on virus replication.  It was soon found that Nef was also a positive virulence factor that contributed to pathogenesis and disease progression in vivo.

HIV genome Nef

The most striking early finding regarding the function of Nef was its ability to cause the removal or downregulation of CD4 from surface of T cells expressing it. The presence of Nef alone was sufficient to produce this effect; no other viral genes were necessary. This led to speculation that the pathogenic role of Nef may result from the downregulation of CD4 expression and/or the disruption of p56Lck signaling in CD4 T cells.

Since then a number of interactions with important host cellular proteins has been discovered, including

  • effects on vesicular transport
  • effects on signal transduction
  • protection of infected cells from lysis by cytotoxic T cells or natural killer cells
  • prevention of superinfection
  • modification of  host cell responses to increase cell survival and thereby increase production of infectious progeny virions.

Now it appears that one of the most significant functions of Nef is to inhibit migration and mobility of HIV-infected cells. For example, Nef-expressing T cells exhibit decreased lymph node homing and decreased extravasation through high endothelial venules (HEVs).  Evidence suggests that this effect may be due, at least in part, to interference with actin function in the cytoplasm of infected cells.

One might speculate that the reduced mobility of infected T cells may promote the interaction of infected cells with uninfected target cells thus increasing the likelihood of virus spreading from cell to cell. Further elucidation of the role of Nef in the mobility of infected cells, and what role this plays in cell to cell transmission, and in viral pathogenesis, will require the development and implementation of new in vivo and in vitro techniques such as multi-transgenic mice, intravital microscopy, and 3D tissue and organ cultures systems. Fortunately significant advances in these areas are being made rapidly.  █

The review article contains a more detailed description of the role of HIV Nef in motility and migration, as well as advances in our understanding of species-specific host factors and cell to cell transmission of HIV-1. Use the link below to access the article.

Adding new dimensions: towards an integrative understanding of HIV-1 spread.
Fackler OT, Murooka TT, Imle A, and Mempel TR. 2014. Nat Rev Microbiol. Jul 16;12(8):563-74.


9 Exciting Advances in Tissue Engineering


Recent advances in tissue engineering are nothing short of miraculous. Several different cells, tissues, and organs have been engineered in the laboratory using techniques ranging from stem cell differentiation to 3D printing. The results achieved to date give hope that even neuronal cells and tissues can be regenerated and used to repair damaged tissues in patients. Here I describe a few exciting examples of recent discoveries and technological advances that I have come across in the science literature within the last few weeks. Continue reading “9 Exciting Advances in Tissue Engineering”

Three Exciting Concepts in Tumor Immunology and Immunotherapy

Report from the Inflammation, Infection, and Cancer and Immune Evolution in Cancer Joint Keystone Symposia, March 9-14, 2014 at Whistler, BC. These symposia focused primarily on the development and immunology of solid tumors. However, there were some very interesting discussions about progress in the treatment of B-CLL and other hematopoietic tumors. 

The mechanisms of survival and progression of solid tumors can be loosely divided into two types: those that affect the tumor itself, and those that affect the immune response to the tumor. Chronic, sub-clinical, asymptomatic inflammation is a conducive microenvironment for tumor development. The effect of tumor factors is contextual and obviously complicated. Factors affecting tumor progression vary from tissue to tissue, tumor to tumor, and individual to individual. Tumors are very good at suppressing immune response, and have evolved multiple mechanisms with which to accomplish this. Some mechanisms may be passive, and some more aggressive. Each different mechanism is quite intricate. As a result there is no one-size-fits-all therapy. Successful treatment requires finding the dominant mechanism in each patient and each tumor. Immunological selection also is involved in tumor establishment and progression. As one investigator put it, we can’t control all the mechanisms, but we can try to control the major ones and hope the rest fall in line.

Following are the three concepts that I found most exciting from the meeting.

1. The tumor vasculature appears to block the infiltration of CD8 T cells into the core of the tumor. Infiltration of CD8 T cells is critical for maintaining tumor “stasis”. In some cases T cells become activated, but can’t infiltrate the tumor.Tumor barrier Several mechanisms by which tumor vasculature can restrict or block access to the core of the tumor were discussed. One possible mechanism that has been observed is that ADAM17 on the surface of Myeloid Derived Suppressor Cells (MDSCs) cleaves L-selectin from the surface of T cells, preventing extravasation of CD8 T cells and entry into the tumor. HMGB1 inhibition decreases ADAM17 on MDSCs and restores L-selectin expression on T cells, providing an opportunity for therapeutic intervention. [Suzanne Ostrand-Rosenberg (1)]. In other cases, tumor endothelial cells have been shown to express FASL on their surfaces. Contact of infiltrating T cells expressing FAS with FASL-expressing tumor vasculature thus leads to death of the T cells when they reach the endothelium. [G. Coukos, (2,3)].

Vascular targeting

2. Targeting cytokines locally. With regard to cytokines, some work which I found particularly exciting was the specific targeting of cytokines to tumor vasculature using the vascular homing peptide RGR conjugated to a cytokine.  (RGR peptide has been shown to associate with angiogenic vessels, 4). This approach results in a more localized effect requiring much less cytokine than systemic administration.  For example, IL-2-RGR leads to prolonged T cell survival within tumors, and primes other immune cells locally. This approach also may be useful for adoptive cell therapy. Another potential and extremely clever use of targeted cytokine therapy is to induce the development of HEV within a tumor essentially creating an ectopic lymph node within the tumor. This would involve the use of the cytokine LIGHT coupled to RGR. [R. Ganss (5)]

3. Adoptive T Cell therapy  with CAR-expressing T cells. Adoptive T Cell Therapy uses ex vivo-activated autologous T cells engineered to express an artificial chimeric antigen receptor (CAR).  CARs target the T cells and their effector functions to specific tumor antigens.  CAR T cellsCAR T Cell Adoptive Immunotherapy has been used successfully for treatment of B-CLL and other hematopoietic tumors, and is currently being evaluated for the treatment of solid tumors. [C. June (6,7)].

Closing Comments

Each individual tumor is unique and shaped by our immune response, which is itself unique to us, and by the initiating mutation or mutations. There are as many mechanisms as there are tumors, and the effect of tumor factors is contextual. However, each mechanism of tumor promotion, escape from the immune system, and metastasis provides a unique opportunity for therapeutic intervention and treatment. The most effective treatments will most likely involve a combination of targets unique to a particular tumor or family of tumors. We may need to treat underlying inflammation, as well as targeting the tumor stroma and vasculature as well as the tumor cells themselves and modulating the immune response. █

1. Hanson EM, Clements VK, Sinha P, Ilkovitch D, and Ostrand-Rosenberg S. 2009. Myeloid-Derived Suppressor Cells Down-Regulate L-Selectin Expression on CD4+ and CD8+ T Cells. J Immunol. 183(2): 937–944.

2. Sata, M. and Walsh, K. 1998. TNFa regulation of Fas ligand expression on the vascular endothelium modulates leukocyte extravasation. Nature Med. 4: 415–420.

3. Sata M, Luo Z, and Walsh K. 2001. Fas Ligand Overexpression on Allograft Endothelium Inhibits Inflammatory Cell Infiltration and Transplant-Associated Intimal Hyperplasia. J. Immunol. 166: 6964-6971.

4. Joyce JA, Laakkonen P, Bernasconi M, Bergers G, Ruoslahti E, and Hanahan D. 2003. Stage-specific vascular markers revealed by phage display in a mouse model of pancreatic islet tumorigenesis. Cancer Cell 4: 393–403.

5. Johansson A, Juliana Hamzah J, Payne CJ, and Ganss R. 2012. Tumor-targeted TNFα stabilizes tumor vessels and enhances active immunotherapy. PNAS 109 (20): 7841–7846.

6. Porter DL, Levine BL, Kalos M, Bagg A, June CH. 2011. Chimeric antigen receptor-modified T cells in chronic lymphoid leukemia. N Engl J Med. 365 (8): 725-33.

7. Grupp SA, Kalos M, Barrett D, Aplenc R, Porter DL, Rheingold SR, Teachey DT, Chew A, Hauck B, Wright JF, Milone MC, Levine BL, June CH. 2013. Chimeric antigen receptor-modified T cells for acute lymphoid leukemia. N Engl J Med. 368 (16):1509-18.

Matched Unrelated Donor Allogeneic Transplantation For Relapsed Diffuse Large B-Cell Lymphoma: Redux

The BMTinfonet group (www.bmtinfonet.org) shared a link to this paper on their Facebook page recently. It’s about the use of allo-stem cell transplant in the treatment of Diffuse Large B cell Lymphoma (DLBCL). The paper was written for scientific and medical professionals who are experts in this field. Even as a scientist with a biomedical background I found the paper difficult to read. The authors use a lot of acronyms and statistical analyses. If you are not a medical professional with a background in bone marrow transplantation, running clinical trials, and/or statistics, you would have a very difficult time plowing through this paper

In this article I will paraphrase the main points of the paper to make it easier to understand. I am not attempting to add anything to the original paper, or to claim any credit for the data, results, or conclusions presented. The original paper is available for purchase at the journal’s website, here:


I also have created a list of acronyms used in the paper, and their definitions, which I will post at the end of this article.

This paper describes a retrospective analysis of DLBCL patients that have received stem cell transplants from either siblings or matched unrelated donors. A retrospective study means it is a historical study. It looks back on, and combines data from, studies that were done in the past. The purpose of this study is to look back on data collected from DLBCL patients evaluated in other studies and see if allo-SCT is a viable treatment option for these patients.

Allogeneic lymphocyte mismatch in a lymph node

In the summary, the authors say that data from 172 unrelated donor hematopoietic cell transplant (URD-HCT) recipients and 301 sib-HCT recipients are compared. This data was extracted from several previous clinical studies and combined. The median follow-up time for which data was available for all the patients was 45 months, or about 4 years. Results of the new data analyses show that the 3-year progression-free survival (PFS) rate was approximately 35% for both groups. Overall survival (OS) was 42% for the sib-HCT group and 37% for the URD group, but these numbers were not statistically different from one another (NS), meaning that no difference between the two groups was found.

The authors note that allo-HCT has only been used for patients that are not good candidates for auto-SCT. This could be because of factors such as extent of disease, resistance to chemotherapy, bone marrow involvement, or those who have failed a previous autograft. Allo-HCT tends to have lower relapse rates compared with auto-SCT, but has a greater risk of complications and mortality other than relapse (non-relapse mortality, NRM). Despite the history of shying away from allo-HCT as a treatment for DLBCL, its use has been on the rise recently due to use of reduced-intensity conditioning (RIC) and better unrelated donor selection.

The main conclusion from this study is that URD-HCT is just as good as sib-HCT for the treatment of DLBCL. This is an important finding because it provides an additional treatment option for patients that do not have a matched sibling available as a donor. This finding also provides doctors with a new opportunity to treat and possibly cure many patients who would not otherwise be considered for allo-HCT.

Original Paper

Avivi I, Canals C, Vernant J-P, Wulf G, Nagler A, Hermine O, Petersen E, Yakoub-Agha I, Craddock C, Schattenberg A, Niederwieser D, Thomson K, Blaise D, Attal M, Pfreundschuh M, Passweg J, Russell N, Dreger P and Sureda A, on behalf of the EBMT Lymphoma Working Party. 2014. Matched unrelated donor allogeneic transplantation provides comparable long-term outcome to HLA-identical sibling transplantation in relapsed diffuse large B-cell lymphoma. Bone Marrow Transplantation (2014), 1–8, advance online publication, 10 February 2014; doi:10.1038/bmt.2014.4.



Allo-HCT Table