Investigating how ebola kills - one receptor at a time

  
   The emergence of a deadly Ebola virus (EBOV) strain into human populations has been our constant worry for over 40 years now. And news of the most recent case where a 12-year-old girl was killed near a major trade hub in Uganda earlier this month only serves to remind us of the devastating impact it can have. Infection with the Zaire strain of EBOV, the one that caused the death of the girl, initially causes a rapid onset of fever and headaches culminating in internal and extrernal bleeding, vomiting and diarrhea and eventually, death. No specific therapy or vaccines are available.

   While Ebola virus Zaire is known to cause up to 90% mortality the exact mechanisms of how it causes disease in humans are not understood. Kondratowicz et al, publishing recently in the journal PNAS, add to our knowledge of EBOV pathogenesis and biology by identifying the receptor molecule (TIM-1) on the surface of our cells that the virus uses to infect humans. 



What is a virus receptor?

EBOV glycoprotein (GP) synthesis and functions. http://www.bio.davidson.edu/

   Viruses are parasites of cells; that is, in order to survive they need to enter our cells and replicate. One major barrier to this, however, is the cell's plasma membrane: an outer covering made up of fats and proteins that protects the cell from the harsh outside environment. On the other hand, viruses have evolved diverse strategies to bypass this barrier and EBOV is not any different (reviewed in TWiV here). Ebola glycoproteins (GP) 1 and 2 lie on the outside of the virus particle and mediate both attachment to the cell via a receptor molecule AND fusion of the virus membrane with the cell membrane releasing the infectious virus genome into the host cytoplasm. This process also appears to involve a peculiar process known as macropinocytosis.


   Viruses do not infect every cell within the human body - they are pretty selective, having adapted their replication cycle to a particular host over hundreds or thousands of years. What then dictates this selectivity? and what role does this host cell choice have on the replication of the virus? The answer lies upon the particular receptor moleculas the viruses use.

EBOV GP structure. http://www.als.lbl.gov/

What about the ebola receptor?


   A number of cell surface molecules have been identified that play a role in the complex process of EBOV entry, all mainly only increasing its efficiency. Although none have been shown to specifically interact and bind to the virus GP 1/2, these may play more of a general role in enhancing entry. How then are we meant to identify what molecules act as specific receptors? More specifically, what does a virus receptor behave like? if we saw one, what would it look like?


   To prove that a particular molecule is a receptor for a specific virus, it should fulfil a set of predictions. Primarily, it must:

• Physically interact with virus proteins (GP 1/2) on it's surface
• Expression of it must significantly enhance infection (shoudn't be found on any cells it can't infect) and if it cannot infect a particular cell, does forced expression restore infectability?
• Removal or blocking of receptor molecule will prevent infection of cell previously susceptable

How did the group do this? 


   To search for the receptor molecule that EBOV uses, Kondratowicz et al sought to correlate EBOV infection with the expression of the receptor molecule. Using a non-related virus (Vesicular Stromatitis virus) that was engineered to express EBOV glycoproteins as well as a green fluorescent protein (GFP), they infected a panel of 54 tumour cell lines. By counting the number of green cells (i.e those that EBOV could enter) they could see which cells were most easily infected and hence expressed the required receptor molecule. 

Percent transduction (GFP expression) of the VSV-EBOV-GP virus (A), Non-EBOV-VSV (B) in a range of cell lines. Correlated with TIM-1 expression date (C).

TIM-1 on the cell surface

   The group then searched through gene expression data corresponding to the cell lines and attempted to pull out a set of candidate receptors common to all susceptible cells, i.e. those that generated a lot of green cells. One gene that they found to be significantly correlated with infection was TIM-1, a type one transmembrane protein expressed on dividing kidney cells and some immune cells. They do note that TIM-1 is not found on all the susceptible cells, suggesting a role for other unknown factors in EBOV entry. Alas the hunt may continue.


   Kondratowicz et al further provides ample evidence that TIM-1 plays a significant role in EBOV glycoprotein mediated entry: he team showed that if you knockdown expression of TIM-1 on the surface of infectable cells with siRNAs, no longer does EBOV infect the cells; they also showed that expressing TIM-1 in cells not previously able to be infected, or ones that weren't all that good at it, allowed the entry of EBOV. Soluble TIM-1 is able to outcompete cell surface TIM-1 for binding to EBOV GP thus causing an inhibition of entry. TIM-1 EBOV GP binding is also demonstrated, fulfilling the requirement of direct interaction between the two. They go on to identify the expression of TIM-1 on the epithelial cells lining the human respiratory tract, a fact important as the means that EBOV initially infects us. Interestingly, the receptor is also found in conjunctiva around the eye. And, finally, infection with viable 'live' EBOV (not the VSV + EBOV glycoproteins) was blocked by administration of an anti-TIM-1 antibody. 

   We may safely conclude that TIM-1 is at least one of the receptors used by EBOV to infect human cells. These results shed light on the possible early events of EBOV infection in humans: aerosolised virus particles entering via the respiratory tract bind to an infect the epithelial cells lining it. From here, further cells are infected, like immune cells, which may allow spread throughout the body. Interestingly, TIM-1 was also found on the conjunctiva indicating a role for hand/aerosol-eye contact mediated infection. 

Death from ebola may soon be a thing of the past. http://www.documentingreality.com/

   This discovery however, does not end the story of the EBOV receptor. Not all cells that can be infected express TIM-1. What receptors are being used in this case? we just don't know yet. What we do know is that we may be on to a worthwile antiviral against ebola. For if we bock virus access to TIM-1 (like what was done in with the antibodies in this experiment) we may be able to severely inhibit EBOV infection and disease.




Kondratowicz AS, Lennemann NJ, Sinn PL, Davey RA, Hunt CL, Moller-Tank S, Meyerholz DK, Rennert P, Mullins RF, Brindley M, Sandersfeld LM, Quinn K, Weller M, McCray PB Jr, Chiorini J, & Maury W (2011). From the Cover: T-cell immunoglobulin and mucin domain 1 (TIM-1) is a receptor for Zaire Ebolavirus and Lake Victoria Marburgvirus. Proceedings of the National Academy of Sciences of the United States of America, 108 (20), 8426-31 PMID: 21536871

The ecology of virus emergence - the role of rodents and biodiversity

   The inter-species transmission of viruses and other pathogens (see data below) poses a serious threat to public health, the global economy as well our environment and biodiversity. Just look at Ebola; SARS and Hendra viruses. With the numbers of emerging viruses increasing year on year, how best are we to deal with this incoming threat? As they say, the most effective bioterrorist is nature herself; so how can we stop her?

Increasing numbers of emerging infectious diseases. Jones et al (2008)

First of all, we can identify a number of possible routes that may be followed if we are to successfully combat or at least limit human infection with other animal viruses. These would include:

• Identifying what viruses may make (or are in the process of making) the jump into humans, i.e. what viruses are out there?

• What are the molecular mechanisms behind inter-species transmission and adaptation?

• Can we identify temporal and geographical (or cultural) 'hotspots' that correlate with increased risk of virus emergence?

• How can we develop potential vaccines/antivirals to further protect vulnerable local/global populations?

And, perhaps most importantly - and the most difficult aspect:

• How are we going to fund this and what are the most cost-effective measures of doing this, i.e can we identify the best places to protect ourselves and place our resources there?

  

Hantavirus - a deadly group of re-emerging viruses. http://virology-online.com/

Deer mouse

   

Orrock et al, publishing recently in the journal American Naturalist, give their contribution to this complex virus protection scheme by identifying key ecological regulators of the potential emergence of a fatal human virus from its rodent species reservoir. Knowledge of this may allow us to pin-point potential danger areas in terms of countries/regions or seasons (by applying their principles to other viruses and ecosystems), which would increase the risk of human infection. By placing emphasis on these areas we could develop a safer, more cost effective strategy to protect at-risk populations.

  

   The model system the group used was that of the rodent-borne hantvirus, Sin Nombre virus (SNV) infecting its host, the deer mouse, Peromyscus maniculatus on the Californian Channel islands. This virus was only relatively recently found to be present among Channel islands deer mice. Hantaviruses are a group of trisegmented negative sense RNA viruses that naturally infect rodent species around the world. Two groups are recognised: one found throughout the new world and the other, throughout the old. When a human is infected by one of the new world viruses (Sin nombre virus, for example), they may develop what is known as hantavirus cardiopulmonary syndrome (HCPS), a life-threatening disease (with up to 50% mortality) caused by leakage of fluids into the lungs. Humans get infected through coming into contact with infected rodents through their aerosolised urine, feces or saliva. In the U.S, the deer mouse (Peromyscus maniculatus) is the primary reservoir of this viruses. Environmental determinants of rodent density are thought to play a significant role in the risk of rodent-human disease through increasing the chances of human/deer mouse contact.

   

Specifically, they obtained SNV-specific antibody data relating to infected mice across all islands, giving them an accurate estimate as to the prevalence of SNV in these mouse populations. The group also compiled data corresponding to a number of environmental factors of these islands, including: area, perimeter, elevation, annual precipitation ( a good correlate with island productivity) and finally the number of deer mouse predators found across the islands. These numbers allowed Orrock et al to determine which ecological factor correlated well with SNV prevalence individually or in combination with others; data that would allow for the prediction of at-risk areas across the islands.

   A number of factors were identified, for example: SNV prevalence correlated well with annual precipitation on the islands as well as island area, which I guess may be expected given that these factors influence the food sources that the mice eat as well as potential space to leave and breed.

   Predator richness negatively correlates with SNV prevalence, suggesting that if we were to artificially remove top predator species from this ecosystem, rodent population density would increase, leading to more and more SNV-infected mice with a greater chance of infecting both themselves and humans. The authors state that the protection of both biodiversity and individual predators within ecosystems would serve to protect human populations from rodent-human virus transmission through the better regulation of host density. Also, environmental increases in primary productivity within the isalnd may also increase the risk of emergence.

   So, Orrock et al have demonstrated the key role of a number of ecological regulators of virus prevalence using a unique island-rodent virus model system. They specifically focused on a potentially fatal virus that can infect humans and hence their work has medical significance within the island system. They have also identified possible situations (bigger islands/more rainfall/low predator richness) that favor an increase in SNV prevalence although, they have not determined exactly why each occurs. This adds to the debate on the relevance of biodiversity to general protection from zoonotic disease.


   This work supplies important evidence for the potential prediction of 'at-risk' regions - not just within the Californian Channel islands - that pose a threat of virus emergence. Seasons with increased rainfall that increase primary production and hence possibly increase rodent densitie. Predictions such as these have recently been used within China and South Korea to identify areas for targeted control of hantavirus infections.

Orrock, J., Allan, B., & Drost, C. (2011). Biogeographic and Ecological Regulation of Disease: Prevalence of Sin Nombre Virus in Island Mice Is Related to Island Area, Precipitation, and Predator Richness The American Naturalist, 177 (5), 691-697 DOI: 10.1086/659632

Interferons, interferons, interferons - what exactly DO they do?

   The interferon (IFN) signalling pathway acts as a primary defense against all viruses through the induction of expression of hundreds of genes following infection; the exact functions of each are, at best, poorly understood. In order to gain a better insight into the antiviral mechanism of the induced genes, Schoggins, et al. (2011) performed a sensitive high-throughput screen of the effects of each one on infection with a range of RNA viruses.

Structure of the IFN-alpha protein. http://www.wikipedia.com/



Abstract:

The type I interferon response protects cells against invading viral pathogens. The cellular factors that mediate this defence are the products of interferon-stimulated genes (ISGs). Although hundreds of ISGs have been identified since their discovery more than 25 years ago^{1, 2, 3}, only a few have been characterized with respect to antiviral activity. For most ISG products, little is known about their antiviral potential, their target specificity and their mechanisms of action. Using an overexpression screening approach, here we show that different viruses are targeted by unique sets of ISGs. We find that each viral species is susceptible to multiple antiviral genes, which together encompass a range of inhibitory activities. To conduct the screen, more than 380 human ISGs were tested for their ability to inhibit the replication of several important human and animal viruses, including hepatitis C virus, yellow fever virus, West Nile virus, chikungunya virus, Venezuelan equine encephalitis virus and human immunodeficiency virus type-1. Broadly acting effectors included IRF1, C6orf150 (also known as MB21D1), HPSE, RIG-I (also known as DDX58), MDA5 (also known as IFIH1) and IFITM3, whereas more targeted antiviral specificity was observed with DDX60, IFI44L, IFI6, IFITM2, MAP3K14, MOV10, NAMPT (also known as PBEF1), OASL, RTP4, TREX1 and UNC84B (also known as SUN2). Combined expression of pairs of ISGs showed additive antiviral effects similar to those of moderate type I interferon doses. Mechanistic studies uncovered a common theme of translational inhibition for numerous effectors. Several ISGs, including ADAR, FAM46C, LY6E and MCOLN2, enhanced the replication of certain viruses, highlighting another layer of complexity in the highly pleiotropic type I interferon system.

  
   The interferons are a multifunctional family of around 20 cell-signaling proteins that are secreted from cells following viral infection (as reviewed here). Our cells expend a lot of energy attempting to detect infection and following this, they express high concentrations of IFN proteins. Following secretion, they bind to receptors - and activate - nearby cells alerting them to the viral assault. 

   Through a complex signaling network a range of genes are actively expressed across the genome that alter the cell in such a way that it becomes harder for viruses to infect them. A rapid antiviral defence system is set-up within the host's tissues and organs. As shown in mice lacking STAT1 a key IFN signal mediator, this IFN signaling network is required to limit viral replication and disease yet also bide time for the development of an adaptive immune response. IFNs are extremely important in our fight against viruses. Only a handful of these IFN-stimulated genes (ISGs) have been characterised while hundreds still sit untouched.

 
What did they do?
 
   Using previously published gene expression data the group chose 389 ISGs for characterisation. To determine what function these ISGs have on virus replication, Schoggins, et al. developed an intracellular assay in which a retroviral vector expressing high levels of both the individual ISG alongside a red fluorescent protein was used to infect IFN pathway-deficient cells in vitro and  then 48 - 72 hours following ISG expression, these exact cells were again infected with a range of RNA viruses expressing a green-fluorescent protein (see figure below). Viruses used included: hepatitis C virus, HIV, yellow fever virus, west Nile virus, Venezuelan equine encephalitis virus and chikungunya virus. 

A) ISG/RFP-expressing retrovirus, B) experimental outline

   

Example results

  Using basic Fluorescent Activated Cell Sorting (FACs) they were able to sort the cells based upon what colour they were, for example: red and the ISG inhibited the virus; green and it did not. More importantly they were able to specifically quantify the levels of green and red to assess the exact levels of virus replication in the cell population. The strongest inhibitors were extensively validated. On top of being expressed individually, some ISGs were expressed in combination to determine whether their antiviral effects were additive. The group were finally able to pinpoint where in the virus replication cycle inhibition took place: entry, transcription, translation, replication or exit.

 The major findings included:

• Most ISGs inhibit virus replication

   As would be expected for an antiviral response, and one which has been shown to already inhibit a wide range of viruses, the majority of the tested ISGs inhibited replication to some degree across a range of viruses looked at. This is a good thing. This means your assay is doing what is supposed to do.

• There are two types of antiviral genes: modest and strong inhibitors

   Owing to how the IFN system has evolved, we may categorise the ISGs into two antiviral classes: modest and strong inhibitors. The modest ones act specifically, targeting limited aspects of the virus replication cycle; the stronger ones function as a positive feedback, increasing the expression of key IFN signaling genes

• Inhibition is additive - more ISGs equals more inhibition

   Upon the activation of the IFN pathway, hundreds of genes are upregulated resulting in an antiviral state within the cell. The defence system is not set up so that protection lies in the hands of a single gene/protein but in the hands of many - it is a truly cooperative process. In this system, following the expression of different combinations of ISGs together within a single cell, the author's noted that inhibition of viral replication increased. 

• Translational inhibition is the most common antiviral mechanism

   The group asked, using a number of assays, at what point do these ISG's inhibit hepatitis C virus replication - is it: entry or translation of HCV mRNA/genome. They found that, in this case, it was not entry but translation. Although, this effect is probably particular to positive-sense RNA viruses. 

• Some ISGs enhanced virus infection

   Interestingly, they found that following expression of a number of ISG's, virus replication increased. Something of a surprise for an antiviral pathway. The mechanisms of why/how these genes did this was not addressed but we can assume that in a real-life infection, the other 380-odd inhibitory genes also upregulated would cancel these out. 

HCV-induced hepatocellular carcinoma. WIll this IFN research aid in potential HCV antivirals? http://www.stanford.edu

Some caveats exist, however:

• Over-expression systems may not reflect in vivo situation

   The results from this work are extremely interesting, important and useful yet the way it was done may not accurately represent what happens when you are infected. Although, I feel that this was not what was set out to be determined by the investigators, which I think were stimulated by the need of novel antiviral candidates. This research will of course aid in that field through the identification of potentially life-saving targets. 

• Only a relatively small number of diverse viruses were screened

   The viruses tested in this system included only a relatively small sample of virus diversity - mainly focusing upon small positive sense RNA viruses (HCV etc.), and one retrovirus: HIV-1. We saw that a number of these ISG's inhibited these viruses but does this reflect what may happen with other viruses? What effect would they have on large DNA viruses, negative-sense RNA viruses or double-stranded RNA viruses? While the fact that the majority of the genes inhibited replication probably wouldn't change, the specifics most likely would. A number of these genes would specifically target pathways and systems that are preferentially used by these small positive sense RNA viruses while some would target those used by other viruses.This experiment would only 'see' those affecting these small positive sense RNA viruses. Although, this may not be a bad thing. These viruses are major causes of morbidity and mortality in both human and other animal populations worldwide.

• Doesn't take into consideration virus IFN modulation

   Every virus probably has different ways of inhibited the IFN response themselves before they are eliminated from the host following ISG expression. This system would not pick up of the majority of these modulatory mechanisms as they occur prior to the expression of ISGs. So, again, as I mentioned before, this work does not reflect what would happen during infection in vivo and nor does it really matter.

Schoggins, J., Wilson, S., Panis, M., Murphy, M., Jones, C., Bieniasz, P., & Rice, C. (2011). A diverse range of gene products are effectors of the type I interferon antiviral response Nature DOI: 10.1038/nature09907

Why should we support WHO Immunisation week?

Currently, children find themselves vaccinated against the harmful effects of myriad different bacterial and viral pathogens: Corynebacterium diphtheriae (diptheria), Clostridium tetani (tetanus), bordatella pertussis (pertussis/whooping cough), polio (poliovirus), hepatitis (hepatitis A and B virus), Haemophilus influenzae, measles, mumps and rubella viruses, pneumonia (Streptococcus pneumoniae), tuberculososis (Mycobacterium tuberculosis) and chickenpox/shingles (varicella zoster virus). Add to these: cholera, human papilloma virus, influenza, meningitis and rotavirus and what you have is a recipe for the improvement of global health.

As many of us in more developed regions of the world rarely come across such things (although it is hard to forget the continuing presence of measles, mumps and influenza across North America and Europe), you may not consider many of these diseases important, yet imagine the effect these pathogens have across the developing world. Think of the young lives lost to these common respiratory pathogens and think of what effect chronic illnesses such as paralytic polio and hepatitis have on not just individuals but communities and families. And, what  must also be remembered is the reason why, we in the developed world, may not come across these terrible diseases - the reason is vaccination. Moreover, the continuing force of rapid and easy global air travel requires us to develop a truly global immunisation effort to prevent the transmission of these pathogens.

 
This week marks the World Health Organisation's (WHO) Immunisation week which has been set up to focus attention on the continuing importance of protecting our children from common yet serious vaccine-preventable diseases. With 180 countries and territories participating worldwide and specifically holding their own weeks in support of this, teams will aim to extend vaccination coverage and support into areas not easily accessible to immunisation campaigns and importantly begin mass-coverage schemes for the likes of measles and polio. But, what is really important here is that this is not just about vaccination, it is about increasing child survival in a broader sense in already under-developed regions and to this effect, vitamin supplements and other medicines are also being distributed.

WHO immunisation week sets out to:

Engaging communities for immunization

Immunization week is led by WHO to:

• vaccinate vulnerable populations, for example those living in border areas and urban fringes;
• raise awareness on the importance of immunization in protecting people against life-threatening illnesses;
• expand the culture of disease prevention and control though vaccination;
• ensure continuing political commitment for immunization

The upkeep of global immunisation requires that the worldwide human population is continuously protected via vaccination, remembering that many of those diseases mentioned above still cause significant illness and deaths in across the developed world. Amazingly, it is not as if we need to develop new vaccines to protect from these diseases; we have them already. Vaccination has proved to be a safe and cost-effective means at reducing the effects of these diseases on the global population so support WHO immunisation week and help raise awareness of just how essential a global strategy to vaccination is.

Can we prevent gorilla extinction with vaccination?

Western Lowland gorilla

Gorillas, Gorilla spp. are found only throughout central African rainforest where there are in total over 200,000 individuals living in the wild. Two gorilla species are recognised, split between east and west Africa with at least two sub-species recognized in both. Their numbers are rapidly decreasing with problems such as habitat loss, poaching and human war contributing  greatly to a rapid reduction in their numbers. Sadly, one other factor on top of these in which these large primates must worry about is that of the transfer of infectious agents arising from humans and other animals. 

Viruses are constantly being transferred between populations of animals but may not establish infection all that easily in a non-host species. Although occasionally infection will result in virus replication and significant disease and this is known as a zoonotic infection -  when non-human viruses are transmitted to humans (see HIV, Influenza A and SARS-coronaviruses) and 'reverse zoonosis' when human viruses infect other animals. This pathogen transfer may be especially important when occurring in a critically endangered species such as gorillas; one recent example is that of human metapneumovirus.



EBOV effects not just humans http://turbo.indyposted.com/



We have been able to detect the effect of a number of viruses on gorilla populations including enteroviruses, adenoviruses and parvoviruses for example, although a small number are known to cause disease. In the last decade thousands of gorillas, chimpanzees and other mammals were killed through infection with the Zaire strain of ebola virus (EBOV) in the rainforests throughout the Congo basin area of central Africa. EBOV is a highly infectious and deadly RNA filovirus which causes a nearly always fatal hemorrhagic fever. The reservoir species for EBOV has been linked to central African fruit bat populations and ebola has caused hundreds of human deaths since its first recorded emergence in the 1970s.  Significantly more non-human primates have been victim to ebola than humans. We can implement a number of control measures for example limiting human-ape contact especially when ill to prevent this virus transfer but this may be more difficult when humans are not involved as in the case of EBOV. There are also a number of therapeutic options available although in the case of ape infection, would be logistically impossible. One strategy we therefore must consider is that of potentially protecting these Gorilla populations through vaccination against a number of potential viral pathogens.



The group VaccinApe is attempting to do just that. A volunteer consortium lead by the charity group the World Wildlife Fund, a vaccine developer Integrated Biotherapuetics and two academic institutions, the Max Plank institute for Evolutionary Anthropology and Kansas state University, VaccinApe is trying to develop an easy and effective method of vaccinating Gorilla populations in the wild. Currently in a 'proof of concept' phase, the group will lead the development of non-human primate vaccinology in order to generate a safe and reliable Ebola virus vaccine to be used through darting of individual gorillas. A large scale vaccination program may therefore afford protection of critically endangered gorilla populations against future EBOV emergences.

In light of the clinical severity of EBOV infection in humans a number of potential vaccine candidates have been developed which rely upon the generation of a protective immune response specifically to EBOV. One main candidate the group are interested in is the EBOV virus-like particles (VLPs). These are effectively non-infectious viruses lacking a viral genome but retaining virus antigenic proteins. Therefore EBOV-specific immunity will be generated against whatever EBOV proteins are found within the VLP. In early trials in macaques, this VLP strategy protected individuals against EBOV challenge although whether this could safely be transferred to gorillas isn't known.

EBOV VLP. Looks and acts antigenically like 'live' ebola. http://www.integratedbiotherapeutics.com/

Endangered wild gorilla and chimpanzee populations are at a great risk from a number of emerging viruses with the most important being EBOV. The difficulties in preventing direct transmission/therapeutic intervention have led people to consider the development of anti-EBOV vaccines. A number of candidates have already been tested and proved safe and effective in non-human primate models possibly allowing these vaccines to be transferred to gorilla population testing. It is hardly surprising that the work required to carry out such large-scale and difficult vaccination campaigns in wild gorillas in the African rain forest will be extremely difficult. The main problems include safety/efficacy testing in gorillas, physical vaccination methods and tracking anti-EBOV immunity non-invasively. Despite these difficulties, only time will tell whether the work of VaccinApe and their partners is to be supported as a worthwhile investment to save these animals.

Le Gouar PJ, Vallet D, David L, Bermejo M, Gatti S, Levréro F, Petit EJ, & Ménard N (2009). How Ebola impacts genetics of Western lowland gorilla populations. PloS one, 4 (12) PMID: 20020045


Richardson JS, Dekker JD, Croyle MA, & Kobinger GP (2010). Recent advances in Ebolavirus vaccine development. Human vaccines, 6 (6), 439-49 PMID: 20671437

Warfield KL, Swenson DL, Olinger GG, Kalina WV, Aman MJ, & Bavari S (2007). Ebola virus-like particle-based vaccine protects nonhuman primates against lethal Ebola virus challenge. The Journal of infectious diseases, 196 Suppl 2 PMID: 17940980

Single Virus Genomics - the future of virus research?

Bacteriophage Lambda particles - like those used in this study

Viruses are the most common organisms on this planet and also most likely the most diverse. It is therefore unsurprising how ecologically important they are in particular environments and indeed global ecological processes. Just look at the amount of papers published on the subject recently. What is preventing us from extending these studies to more environments and preventing us having a closer look at what viruses are present is our inability to study small amounts of these microorganisms. Our knowledge of global viral diversity has most likely been biased by this lack of single-virus investigations.

Metagenomics?

In order for us to study viruses at the molecular level we have to somehow get the virus. This usually requires infecting certain cells with the virus in order to take advantage of virus replication and produce more and more copies of viral particles. This means that we have to find cells that the virus infects, which is difficult for some viruses found in environmental samples where no knowledge of host is available. This problem has been encountered with bacterial species where it was found that we were only able to grow in the lab a small percent of the total microbes from a single sample. The field of bacterial 'metagenomics' (get your free pdf review here) took off when it became easier and easier to study the molecular biology of those bacteria without the need to grow them in the lab; we are now able to fully sequence bacterial genomes without the need for culturing. These developments are now being applied to virus species in a diverse range of environments.

Single Virus Genomics (SVG)

A recent study in PLoS ONE reports the development of a strategy to overcome such problems; Allen LZ et al (2011) - of the J. Craig Venter Institute - show, in a 'proof-of-principle' study, how they can now separate individual virus particles from a mixture and submit these single viruses to genomic analysis. The results of this paper are likely to enhance many areas of virology including ecology, immunology and basic biology which is probably why the group have patented the process. Although the paper didn't actually deal with environmental samples, a paper by the same group is currently in the works.

SVG strategy: seperate, agarose and PCR

What Allen et al did was make themselves a well defined mixture of bacteriophage (viruses of bacteria) particles. They filtered this suspension in order to only get the viruses in their sample. These viruses were then dyed by the attachment of fluorescent molecules to their surfaces so as they could be separated using what is known as a flow cytometry machine. This machine allowed only single virus particles to pass through and were then 'printed' onto a microscope slide in a 'high-throughput' fashion. To stabilise the particles they embedded each virus in a bead of agarose - a gel-like substance; they were also able to visualise each virus found within the agarose. Once they had separated each particle out they then used a special kind of PCR to amplify the entire virus genome inside each agarose bead. The products of this were then used for DNA sequencing and finally assembled into the whole virus genome using computational methods.

The group are currently attempting to further optimise this protocol to make it easier and more accurate especially considering that this method cannot yet be easily used for RNA viruses nor viruses about which no sequence information is known. Also, the viruses amenable to this technique would have to be pretty stable to survive the whole process. You can read about their plans for this in the paper's discussion.



A single bacteriophage particle

What does this mean for virology in general?

Virologists have generally concentrated on studying populations of viruses in their investigations; animals or cells are infected with one million infectious virus particles and the effects on host functioning are measured, for example. What this research shows is that in some cases it is entirely possible to look at the genome of individual particles and not have to rely upon mixtures of thousands, if not millions, of genetically variable viruses. The major areas of science that may benefit from this development will be those that rely on virus discovery, for example, the assessment of total virus diversity in a given environmental sample. The ability to uncover low concentrations of virus in an infectious disease context in humans may also benefit, especially if there is difficulty in growing the virus in tissue culture. Groups studying the genetic diversity of viruses can now accurately determine the exact genome sequences of individual viruses and also quantify them. This research will hence benefit a wide range of disciplines within virology in general.


 

Allen LZ, Ishoey T, Novotny MA, McLean JS, Lasken RS, & Williamson SJ (2011). Single virus genomics: a new tool for virus discovery. PloS one, 6 (3) PMID: 21436882

Is that an Ebola virus superantigen I see?

The process in which a virus causes disease and dysfunction within its host is termed viral pathogenesis; the study of which is pretty important if we are to fully understand infection, replication and transmission of pathogens as well as to develop effective antivirals and vaccines. Ebola virus (EBOV) is one such deadly virus in which there are currently no approved antivirals nor vaccines and which the study of pathogenesis is therefore ever more important. 

EBOV particle. www.accessexcellence.org

First isolated in the late '70s, EBOV now causes significant epidemics occurring with increasing frequency - the latest in early  2009. It is  believed that bats play an important role in the natural replication cycle of these viruses and hence may transmit it to neighboring human and other animal populations. There are currently four 'species' of EBOV recognised which infect humans: Zaire, Sudan, Ivory Coast and Bundibugyo - yet a fifth related virus, EBOV-Reston is known only  to infect non-human primates in captivity and domesticated pigs. These viruses which are mainly found throughout Central and Western Africa cause a hemorrhagic fever in humans which most often or not leads to death; EBOV-Zaire (ZEBOV) is the most deadly of all types resulting in at most 90% of those infected to die; the reasons for such high mortality are not known.

We can begin to build up a picture of ZEBOV infection and pathogenesis using a combination of in vitro studies, animal models and clinical work carried out in humans. In animal models EBOV has been shown to replicate to extremely high levels, induce the abundant secretion of inflammatory signalling molecules, cause massive cell death of lymphocytes and a great deal of tissue destruction eventually leading to multi-organ system failure, toxic shock and death. Work carried out on blood samples collected from both human survivors and non-survivors of EBOV outbreaks have showed that lethal infection is associated with a highly deregulated immune response. Extremely high levels of pro-inflammatory cytokines (cell signalling proteins) were detected as well as low levels of circulating T lymphocytes. Yet there was a surprisingly little anti-viral response seen. This all suggests that the EBOV induces a rapid and strong pro-inflammatory immune response without eliciting effective innate and adaptive antiviral defenses resulting in a lethal outcome. Those people which did not develop this lethal immune reaction survived EBOV infection. But how exactly does EBOV do this?

New evidence has been uncovered suggesting that certain ZEBOV components may act like what are known as 'superantigens' (sAg) which may responsible for this damaging deregulation in immune responses.

Superantigen TCR/MHCII interaction. anagen.ucdavis.edu

As the paper explains:

"SAgs are microbial proteins that bind simultaneously to major histocompatibility complex class II molecules and to the T-cell receptor (TCR) V beta region. This “bridge” skews the T-cell repertoire by amplifying specific T- cell V beta subsets, which then are either rapidly deleted by activated cell death or become anergic."

What this means is that maybe ZEBOV proteins are able to bind to our own immune cells through an abnormal mechanism (TCR AND MHCII) which results in those cells going into overdrive and then being selectively killed by our bodies (in order to prevent a runaway immune response) or those cells becoming immunologically unresponsive (anergic). If EBOV did encode a sAg it may be able to vastly eliminate our adaptive immunity.

Vbeta region mRNA expression levels in ZEBOV infected patients

A major feature mentioned above is the massive levels of cell death in T lymphocyte populations. There are many ways in which EBOV could produce this effect, including up regulation of pro-cell death molecules inside lymphocytes or through an alternative indirect pathway via infection of dendritic cells and macrophages - as it is known EBOV infects these cells. These immune regulatory cells are responsible for controlling the levels of other immune cells produced (they are considered major immunoregulators)- alter their behavior and you alter the number of lymphocytes. The finding the EBOV may encode a superantigen adds to the growing number of ways this virus may inhibit host immune responses.

We can begin to investigate this by looking at the specific types of T cell found within EBOV infected patients - normally you would expect each T cell V region type to found to the same level. sAG activity leads to the loss of specific T cell types without loss of others. Looking at the expression levels of specific V regions of the TCR we can observe whether certain types decrease after being infected with EBOV. This recent report demonstrated just this in infected patients versus non-infected (see above) suggesting that something in EBOV may act as an sAg. This appears to correlate well with a fatal immune response. 

Of course we will have to further verify this finding possibly in animal models or cell culture work but we can begin to ask further questions: does this occur in other EBOV species? What protein is causing the sAg activity? Can we somehow inhibit its activity? And, how is it that some patients come to avoid a sAg response?

Leroy EM, Becquart P, Wauquier N, & Baize S (2011). Evidence for ebola virus superantigen activity. Journal of virology, 85 (8), 4041-2 PMID: 21307193


Wauquier N, Becquart P, Padilla C, Baize S, & Leroy EM (2010). Human fatal zaire ebola virus infection is associated with an aberrant innate immunity and with massive lymphocyte apoptosis. PLoS neglected tropical diseases, 4 (10) PMID: 20957152

On the origins of smallpox - where and when did variola virus emerge?

2011 may be the year where the last known officially acknowledged stocks of the deadly smallpox virus, variola are destroyed - a virus that claimed over 500 million lives in the 20th century alone. The extensive collection of 'live' virus and DNA stocks totalling over 500 isolates/strains, which are held between the US Centres for Disease Control and the Russian State Research Centre of Virology and Biotechnology may be ordered to be eliminated following World Health Organisation (WHO) recommendations soon to be announced.

Although the impending fate of this pathogen has been covered elsewhere by Vincent Racaniello and Steven Salzberg I have been led to ponder its beginnings, at least in humans: where and when, over the course of human history did variola virus emerge  and have we always suffered from it? What confuses the matter further is that there are two clinical forms of smallpox - major (30% mortality) and minor, including both African and Alastrim minor (<1% mortality)- do these viruses have the same evolutionary history and if so, when and where did they diverge? Luckily, we can now study the origins of infectious diseases through both molecular and historical records.

A depiction of Shapona the west-African Yoruba god of smallpox. Courtesy James Gathany (photo), CDC/ Global Health Odyssey.

Conflicting historical records

It has been very confusing trying to make sense of the historical records of suspected smallpox cases as there are significant gaps in documentation and many conflicting reports. Smallpox-like skin lesions have been observed on Egyptian mummies dating from as far back as 1580 B.C yet there is no mention of the disease at all in the Old or New testaments nor even the Hippocratic texts. There was some mention of a smallpox-like disease in China and India as early as 1500 B.C but the only unmistakable description can be found from the 4th century A.D in China.  Interestingly there was no mention of smallpox in the American continents nor in sub-Saharan Africa prior to European exploration. But as shown in the picture above, smallpox has shaped west-African culture. So, did smallpox originate in Asia and spread to Egypt around 1,500 B.C? Or, is smallpox a relatively recent human disease, emerging around the 4th century A.D in Asia?

Molecular data shed light on variola evolution

A 2007 study using genomic data from the CDC's variola collections - the same ones that may soon be destroyed, added a phylogenetic perspective to the origins of smallpox and how it spread worldwide. Through studying single nucleotide polymorphisms (SNPs) from 47 variola genome isolates from geographically distant areas and collected between the 1940s and '60s they examined the genetic relatedness between isolates and were able to estimate the time since they shared a last common ancestor. They combined this DNA evidence with the above historical records to generate an idea as to where, when and how smallpox originated and spread throughout human populations.

Variola genome phylogeny

Abstract: Human disease likely attributable to variola virus (VARV), the etiologic agent of smallpox, has been reported in human populations for >2,000 years. VARV is unique among orthopoxviruses in that it is an exclusively human pathogen. Because VARV has a large, slowly evolving DNA genome, we were able to construct a robust phylogeny of VARV by analyzing concatenated single nucleotide polymorphisms (SNPs) from genome sequences of 47 VARV isolates with broad geographic distributions. Our results show two primary VARV clades, which likely diverged from an ancestral African rodent-borne variola-like virus either ≈16,000 or ≈68,000 years before present (YBP), depending on which historical records (East Asian or African) are used to calibrate the molecular clock. One primary clade was represented by the Asian VARV major strains, the more clinically severe form of smallpox, which spread from Asia either 400 or 1,600 YBP. Another primary clade included both alastrim minor, a phenotypically mild smallpox described from the American continents, and isolates from West Africa. This clade diverged from an ancestral VARV either 1,400 or 6,300 YBP, and then further diverged into two subclades at least 800 YBP. All of these analyses indicate that the divergence of alastrim and variola major occurred earlier than previously believed.

Hypothesised spread of variola worldwide

When analysed, variola fell into two large monophyletic clades signifying a historical divide in their genetic relatedness. The earliest representative - or most basal - of the variola major smallpox viruses are the Asian isolates. This suggests that major may have originated in Asia followed by geographic radiation across the Old world and into Africa. Using historical records as a means to calibrate variola evolutionary history, their results indicated that smallpox spread from Asia as much as 1,600 years ago which neatly backed up the historical records of 4th Century China. By the time smallpox reached out of East-Asia, the ancient Greek and Roman civilisations were no more - hinting that the reason they didn't observe smallpox was because at that time, in the Mediterranean region there wasn't any variola virus transmission. Despite this, analysis of the second major clade suggested a split 6,300 years ago placing variola well into ancient history. So, is smallpox a very old or relatively recent human pathogen? And, if so, where did it occur? The molecular data also showed that the clinically 'minor' forms of smallpox - African minor and Alastrim minor are very much related to the major viruses; evolutionarily speaking these viruses are thus very smilier.

A rodent origin of smallpox?

We can investigate the origin of smallpox through the molecular characterisation of other poxviruses. Variolataterapox virus) and camelpox viruses and they all are more related to each other than to other poxviruses, such as monkeypox. When their genomes were compared to that of variola, a time since divergence was estimated at between 16,000 and 68,000 years ago. As taterapox and camelpox are primarily found throughout Africa and Asia this suggests a possible origin of variola and the other poxviruses from ancient endemic poxviruses in Africa, possibly from rodents. Upon human infection this virus may have followed us out of Africa entering Asia and spreading across the globe. Or possibly, the virus emerged in rodent populations only to pop up again in Asia thousands of years later.

Although this period is quite a bit before the development of human agriculture and increased population density as is possibly required for such a highly infectious and lethal virus like smallpox to persist, the ancient variola virus might have behaved very differently from the one we know and fear. Sadly, we cannot say for sure exactly how and where variola emerged because we simply do not know a lot about the natural diversity of poxviruses in rodents or other mammal species and until we do, we will not have an accurate answer.

Future Pox?

Monkeypox from bushmeat? www.lynnjohnsonphoto.com/

What does this history of smallpox say about its impending eradication and the threat of a future virus emergence? Well, sometime in our ancient past variola virus emerged into prehistoric human populations and the data indicate that this may well have occurred within the African continent or nearby in Asia and it is likely that this same ancestral virus emerged into other mammalian species, such as Camels and Rodents. Smallpox then might have followed us through our journey out of Africa and became endemic in large population centres across the Eurasian landmass.

Although we have now effectively eradicated variola from the human population - and soon seek to destroy its last remaining stocks - might another poxvirus emerge just like it did before? We are now in a situation where the human population has very little immunity to variola and other related poxviruses, a situation which last would have existed prior to the initial emergence of smallpox. This provides ample breeding ground for novel poxviruses to emerge and fill the niche emptied by waning population immunity. Alarmingly, the rate of monkeypox infections - another rodent poxvirus - has been increasing (20X)  in the last 3 decades following cessation of smallpox vaccination. May this, or another related poxvirus, be the new smallpox? Could existing smallpox stocks not be used to study poxvirus/human interactions? May it be premature to destroy them in light of possible future pandemics? Only the WHO can decide later ths year.

Gubser C, & Smith GL (2002). The sequence of camelpox virus shows it is most closely related to variola virus, the cause of smallpox. The Journal of general virology, 83 (Pt 4), 855-72 PMID: 11907336

Li, Y., Carroll, D., Gardner, S., Walsh, M., Vitalis, E., & Damon, I. (2007). From the Cover: On the origin of smallpox: Correlating variola phylogenics with historical smallpox records Proceedings of the National Academy of Sciences, 104 (40), 15787-15792 DOI: 10.1073/pnas.0609268104

Raymond S. Weinstein (2011). Should Remaining Stockpiles of Smallpox Virus (Variola) Be Destroyed? Emerg Infect Dis, 17 (Apr) : 10.3201/eid1704.101865

Rimoin AW, Mulembakani PM, Johnston SC, Lloyd Smith JO, Kisalu NK, Kinkela TL, Blumberg S, Thomassen HA, Pike BL, Fair JN, Wolfe ND, Shongo RL, Graham BS, Formenty P, Okitolonda E, Hensley LE, Meyer H, Wright LL, & Muyembe JJ (2010). Major increase in human monkeypox incidence 30 years after smallpox vaccination campaigns cease in the Democratic Republic of Congo. Proceedings of the National Academy of Sciences of the United States of America, 107 (37), 16262-7 PMID: 20805472