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HIV & Measles – double hit pathogenesis?

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Despite ongoing worldwide eradication efforts, measles infection still results in significant morbidity and mortality. Although, throughout most of the developed world measles infection has been considerably reduced there still exists massive (and deadly) outbreaks in areas such as Africa and South-East Asia. Investigation of the reasons why this disparity occurs therefore  is of major medical, political and social interest.

Many factors are likely to be behind this major difference – and all of which deserve our attention if we are ever to remove measles from the human population. There exists problems in rolling out vaccines in countries with poor infrastructure such as roads and transport facilities; disruption to what is known as the vaccine ‘cold-chain’ (vaccines have to be kept cold to avoid rendering them unusable) is likely to occur; general poor health of the population in these regions and possible interference of vaccination in children with high levels of passively acquired maternal antibody.

Measles vaccination efforts in Africa may not be entirely effective

Today in PLoS Pathogens, Nilsson and Chiodi highlight in a featured opinion article, another possible source: the link between co-infection with HIV-1 and Measles infection. They point out that HIV-1 infection and replication may result in impaired immune responses in both mothers and children leaving open the possibility of measles infection (no immune system, no protection). HIV-1, as I’m sure you will all know, is a potentially deadly pandemic retrovirus – particularly a major problem in sub-Saharan Africa- which infects humans where it resides in the bodies own immune system: T cells, dendritic cells and macrophages. Viral replication results in the death of these immune cells and destruction of important lymphoid tissues resulting in an individual without key immune functions.

The authors note that children born to mothers who are HIV-1 positive or are HIV-1 positive themselves develop lower levels of anti-measles antibody upon vaccination -a big deal if we’re looking to protect these kids through vaccination. They show that memory B cells may be impaired and lower protection will result through failure to mount a B cell-generated antibody response. Immunity is a highly regulated system, if you remove one aspect-  in this case T cells – you will affect another pathway , in this case B cells. Thus there exists a major  problem with HIV-1 infected people and infection with other pathogens in the environment; HIV-1 infection significantly alters the host immune system weakening it to other invading pathogens such as measles which is endemic in these areas.

So how do we overcome this problem? Well, the authors suggest that on top of increasing vaccination coverage through catch-up programs it would be wise to administer anti-retroviral drugs  to mothers and children prior to vaccination to allow sufficient immune function; this should hopefully make a difference in combating both measles and HIV in the developing world, especially in an area where both cause so much pain. Hopefully, strategies such as this will aid treatment efforts for other pathogens rife in the developing world – targeting both HIV and the individual agents may be more effective.

Sadly, there exists another interaction between HIV and co-infection with other pathogens. Infection usually results in increased levels of immune cells in the blood and tissues yet these very cells are the target for HIV and if these cells increase, HIV replication will also. There exists a deadly interaction between multiple pathogens which must be broken.

Nilsson, A., & Chiodi, F. (2011). Measles Outbreak in Africa—Is There a Link to the HIV-1 Epidemic? PLoS Pathogens, 7 (2) DOI: 10.1371/journal.ppat.1001241


Written by Connor

February 11, 2011 at 3:05 pm

The molecular domestication of amphibian retroviruses – do they play a physiological role?

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ResearchBlogging.orgWe mostly think of viruses of being ‘bad’ and ‘dangerous’ yet there are countless examples of viruses playing a positive role in their host’s life. These symbiotic agents have been co-opted by the host to do something good; some viruses have even been inserted into our genomes and thus are forever tied to our germline and our descendants – sometimes even these viruses can do good. This is the kind of game evolution plays with our viral parasites and us – its generally pretty cruel and inconsiderate but every so often we get something good out of it.

Xenopus tropicalis - do recently identified ERVs play a functional role?

One example of these endogenous viruses is the endogenous retroviruses or ERVs, which are somewhat related to the non-endogenous – ‘exogenous’ – retroviruses that can cause disease in us and other animals (HIV XMRV?). Just to put it into perspective, 8% of our genome is made up of these ERVs and they also make up a large chunk of other vertebrate genomes. The majority of these inserted retroviral genomes have been destroyed by the forces of evolution and thus bear little resemblance to their ‘wild’ cousins; they are not expressed and their sequence shows little homology to other retroviruses. However, some ERVs have changed very little, suggesting an important function may be conserving them – these are expressed and do sort of resemble the exogenous ones. The insertion of a novel ERV sequence into a host’s genome acts as evolutionary raw material allowing significant adaptive functions to arise and a great deal of evidence suggests they can these can even play a physiological role in host biology – this is known as molecular domestication. One interesting example is the ERV role in the mammalian placenta.

Chromosomal location of the Xenopus ERV-like sequences

A recent paper reports the discovery and characterisation of an amphibian ERV whose genomic organisation is highly conserved making it a good candidate to have a novel physiological function. Investigating the genome of Xenopus tropicalis – an ‘African clawed frog‘, the group discovered a unique DNA sequence that was highly related to a previously characterised Xenopus protein with frost-resistant functions – allowing winter survival in woodland frogs. This 9,551 base-pair DNA sequence not only contained the intact frost-resistant gene but also a full-length retroviral genome with the general organisation of many common ERVs – 5’ LTR-GAG-POL-ENV-3’LTR.

ABSTRACT: We report on the identification and characterization of XTERV1, a full-length endogenous retrovirus (ERV) within the genome of the western clawed frog (Xenopus tropicalis). XTERV1 contains all the basic genetic elements common to ERVs, including the classical 5′-long terminal repeat (LTR)-gag-pol-env-3′-LTR archi- tecture, as well as conserved functional motifs inherent to each retroviral protein. Using phylogenetic analysis, we show that XTERV1 is related to the Epsilonretrovirus genus. The X. tropicalis genome harbors a single full-length copy with intact gag and pol open reading frames that localizes to the centromeric region of chromosome 5. About 10 full-length defective copies of XTERV1 are found interspersed in the genome, and 2 of them could be assigned to chromosomes 1 and 3. We find that XTERV1 genes are zygotically transcribed in a regulated spatiotemporal manner during frog development, including metamorphosis. Moreover, XTERV1 transcription is upregulated under certain cellular stress conditions, including cytotoxic and metabolic stresses. Interestingly, XTERV1 Env is found to be homologous to FR47, a protein upregulated following cold exposure in the freeze-tolerant wood frog (Rana sylvatica). In addition, we find that R. sylvatica FR47 mRNA originated from a retroviral element. We discuss the potential role(s) of ERVs in physiological processes in vertebrates.

Following the characterisation of the genome sequence, the group looked whether there any more ERVs like this one in Xenopus genomes  to see if  this a rare example of a highly conserved ERV and were there any other examples of these sequences present? There turned out to be 59 genomic loci with some sort of homology to the newly found ERV however all had significant mutations present rendering them functionally inactive – at least where gene expression is concerned. These sequences were mapped onto Xenopus chromosomes, showing that the intact ERV was present on chromosome and the ‘damaged’ ones were found throughout the genome. This ERV is after all a lone agent in the Xenopus genome – confirmed by these experiments. Phylogenetic studies were also carried out which suggested that primary retroviral integration occurred roughly 41 million years ago and from then on multiple rounds of movement around the genome or reinfection generated the many mutated copies around the genome. Their results also suggest that this ERV is actively replicating and inserting itself into the genome up to the present day. A cousin of this retrovirus was also found in the closely related X.laevis genome showing that integration occurred prior to the evolutionary separation of these two lineages.

Expression of ERV sequences throughout Xenopus development and time

They next turned their attention to whether this ERV had a functionally active role (is it transcribed; in what tissues and at what points in frog development?) in host biology as observed in other host/ERVs. Using real-time PCR and in situ hybridisaton techniques, the group were able to follow ERV expression throughout X. tropicalis development and assess the level of transcription and tissue localisation and possible infer a physiological function. They noted a highly regulated yet dynamic expression of gag, pol and env expression from fertilisation through metamorphosis (curiously a peak of activity was seen during metamorphosis) and adult life but does this control of expression actually mean something functional or is it merely physiological neutral? This ERV may just be replicating within the host genome without contributing something to host life. In order to understand this, they subjected X. tropicalis tadpoles or cell lines to a number of biological ‘stresses’ e.g. metabolic, temperature and UV stresses. An upregulation of ERV expression was seen upon metabolic and UV stresses and not in temperature – suggesting a fine tuning of its expression in response to a number of stresses. Whether this actually achieved something functionally was not investigated.

A recently discovered retrovirus derived gene in another frog species was found to play a role in protecting frog cells from the effects of freezing conditions. This study, on the backs of that investigation determined that frost-tolerant gene was derived from a highly conserved ERV present within Xenopus genomes. A distinct physiological role for these ERV-derived genes was not validated in this study yet in the future, further characterisation of its expression in vivo under temperature stress should be undertaken. This work underlines the importance that retroviruses and their endogenised cousins play in host cell functioning and evolution. Viruses are not all bad news – sometimes they can help you.

Roossinck, M. (2011). The good viruses: viral mutualistic symbioses Nature Reviews Microbiology, 9 (2), 99-108 DOI: 10.1038/nrmicro2491

Sinzelle, L., Carradec, Q., Paillard, E., Bronchain, O., & Pollet, N. (2010). Characterization of a Xenopus tropicalis Endogenous Retrovirus with Developmental and Stress-Dependent Expression Journal of Virology, 85 (5), 2167-2179 DOI: 10.1128/JVI.01979-10

Written by Connor

February 10, 2011 at 11:39 am

Studying viral infection at the whole-organism level

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Some questions about how viruses cause disease in their hosts (viral pathogenesis) are best asked and studied using an in vivo model system; just sometimes infecting cells under tissue culture conditions just doesn’t cut it. Questions like: how does a virus interact with all the immune cells during an infection and what cells does the virus actually infect should be asked this way.

But of course, this in vivo stuff is a great deal more difficult than in vitro studies and appropriate animal models don’t just grow on trees; this is why, when a relevant model system of viral infection comes along we get excited – well at least I get excited. Unless you look at everything in its entirety, you never know what you will miss and viruses being as small as they are, its easy to miss something important and missing something important is bad news in the world of science.

A recently published study has looked at viral infection at the ‘global’ or whole-organism level using transgenic zebrafish larva infected with Infectious Hematopoietic Necrosis Virus (IHNV), an RNA virus related to rabies virus and is particularly deadly if you happen to some form of salmonid. Zebrafish are generally pretty good models for a whole lot of biological processes: zebrafish genetics are pretty well understood allowing for easy transgenics; they are particulary easy to study, especially to image as they are small and transparant and some genes/pathways are well conserved with humans meaning that it may have some applications to us. These factors all suggest that zebrafish may be a pretty decent model to understand viral infection in general, not just in fish.

Following infection, they were able to look at entire whole organisms for viral presence, concentrating on what particular cells/organs contain viral mRNA  and proteins. They were able to follow infection through its entirety, at early stages and the later stages when serious disease takes hold, allowing the elucidation of intra-host viral spread and dissemination. They used their system to shed light on the mechanisms of IHNV pathogenesis, showing that viral infection led to vascular endothelium destruction and impaired blood flow. It is just near impossible or at least a lot of hard work to do this kind of analysis in any other model system.

Zebrafish viral infection: In blue are cell nuclei, green endothelial cells and red viral proteins.

Using this model – as in all model systems – comes with certain caveats attached: IHNV is not a natural pathogen of zebrafish (indeed, to date no viruses have been described) , i.e. what we see here may not be exactly what happens out there in the real world when this virus infects salmon. The virus was also injected into the bloodstream of these fish which is highly unlikely to occur in the wild – how would the infection change if it were administered another way? Not considering these issues, this work offers up a decent picture of systemic dissemination of IHNV in a not-so-perfectly matched host. Only time will tell how applicable to the real-world this is.

Its hard to imagine this work being carried out in any other kind of vertebrate – transparent rats in the future perhaps? But this stuff has been carried out using GFP expressing viruses within a non-human primate model only a week before this. Although not as easy to image, hard-work and dedicatedly searching through cells and tissues for signs of infection allows us to understand viral infection at the whole-organism level more appropriate to human disease.

This pretty much makes their statement below a bit incorrect, or at least out-dated:

We describe in this paper the spread of a viral infection throughout an entire organism, something that, to our knowledge, has not been done before in a vertebrate.

As a final thought, wouldn’t it be great to image viral infection in real-time using a GFP-expressing IHNV in this zebrafish model? – just checked, there is a GFP IHNV virus out there. Check out the live-cell imaging of GFP neutrophils in a zebrafish above.

Two Zebrafish larvae

ResearchBlogging.orgLudwig, M., Palha, N., Torhy, C., Briolat, V., Colucci-Guyon, E., Brémont, M., Herbomel, P., Boudinot, P., & Levraud, J. (2011). Whole-Body Analysis of a Viral Infection: Vascular Endothelium is a Primary Target of Infectious Hematopoietic Necrosis Virus in Zebrafish Larvae PLoS Pathogens, 7 (2) DOI: 10.1371/journal.ppat.1001269

Ludwig, M., Palha, N., Torhy, C., Briolat, V., Colucci-Guyon, E., Brémont, M., Herbomel, P., Boudinot, P., & Levraud, J. (2011). Whole-Body Analysis of a Viral Infection: Vascular Endothelium is a Primary Target of Infectious Hematopoietic Necrosis Virus in Zebrafish Larvae PLoS Pathogens, 7 (2) DOI: 10.1371/journal.ppat.1001269

Written by Connor

February 5, 2011 at 12:00 pm

Can fluorescent-‘labelled’ viruses illuminate their mechanisms of pathogenesis?

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Have you ever wanted to visualise viral infection? Ever wanted to observe how they enter and spread throughout their host organism? Ever wanted to know how exactly they caused disease – at the cellular and whole-organism level? Well, this may be entirely possible using fluorescent-labeled recombinant viruses infecting a relevant model system.

GFP-virus infected cells

So how does it work?

Lemon et al recently report the continued investigation of measles virus pathogenesis in a non-human primate (Macaque) model utilising a green-fluorescent protein (GFP) expressing virus. Upon infection of host cells, viral transcription leads to the very high expression of GFP, flooding the cytoplasm with this fluorescent ‘tag’. Subsequent microscopy, imaging and immunohistochemistry allows for the identification and location of the infected cells, tissues and organs – see image above. Tracking of cellular infection allows us to decipher the development of MeV entry, spread and replication at both the cellular and whole-organism level throughout the entire infection. Studies such as these give an unprecedented view of viral infection in a means directed related to that of human infection. This model even allows for macroscopic real-time detection of fluorescence and hence viral infection.

Why is this important for measles?

Despite a highly effective vaccine and significant global control initiatives, measles infection still accounts for significant morbidity and mortality worldwide, mostly in the developing world (164,00 deaths in 2008). This is mostly attributable to the profound immunosuppression induced allowing for further infection with opportunistic pathogens. Currently, much is known about measles pathogenesis yet the molecular mechanisms of such are poorly understood and it is therefore of great interest to better understand these processes by which MeV infects and causes disease in humans. Knowledge of such may facilitate the development of more effective and safer vaccines for measles and indeed other viral pathogens.

Viruses being obligate intra-cellular parasites, must enter and exit cells in order to survive. Most of viral pathogenesis can therefore be attributed to the effects of viral replication of host cells and tissues; a major determinant of which is the expression of receptors on host cells surfaces allowing viral entry, infection and replication. Currently only a single receptor – CD150 – (otherwise known as signalling lymphocyte activation molecule SLAM) has been discovered that wild-type pathogenic MeV uses to enter host cells; the distribution of which only explains part of measles pathogenesis as epithelial and neuronal cells (important target cells) do not express the protein. As indicated by this receptor being expressed on lymphocytes and other immune cells, MeV is a highly lymphotropic virus! But if epithelial cells fail to express the receptor on their surface, how come its possible for MeV to enter via these cells?

The classical view of measles pathogenesis was that free-virus entered the host through the respiratory route, infecting and primarily replicating within the epithelial cell lining of the respiratory tract. Newly produced virus spreads to nearby lymph nodes where infected monocytes – a type of immune cell – facilitates viral dissemination throughout the host, resulting in the well-known symptoms of measles. The problem with this being that epithelial cells and unstimulated monocytes fail to express the MeV receptor CD150 and infection should therefore not occur. Recently, it has been shown (again using a GFP expressing virus in a macaque model) that MeV predominately infects dendritic cells during the peak of infection, ruling out a major role for monocytes. There is also however no direct evidence of MeV primary replication within the epithelium of the respiratory tract at the early stages of infection. So what exactly happens during the start of infection and does it develop? GFP-expressing viruses may shed light on this question.

Diagramtic representation of the cellular composition of the human respiratory tract - notice the epithelial cell lining and the alveolar macrophages. Dendritic cells are however not shown on this diagram.

Diagramatic representation of the cellular composition of the human respiratory tract - notice the epithelial cell lining and the alveolar macrophages. Dendritic cells are however not shown on this diagram.

So how can we study the early stages of infection?

The incubation period of  measles is about 2 weeks in humans making it particularly difficult to study the early events of viral infection – the kind of events like host entry, initial site of replication and subsequent intra-host dissemination – this is where we can use a non-human primate model.

Lemon et al  generated a highly virulent recombinant MeV based on viral isolates from an outbreak in Sudan; they engineered the viral genome so that it expressed GFP upon entry into cells – an addition that causes little or no replication defects to the virus. Groups of macaques were subsequently infected via the respiratory route allowing highly sensitive visualisation of GFP expressing cells following necropsy. The early time-points of around 5 days post infection were focussed on in this investigation allowing the determination of the early cell targets – epithelium? Immune cells?

So what did they find?

Their results suggest that at the early stages of MeV infection, GFP and hence viral replication is only found in immune cells within the respiratory tract and not the epithelial lining. Dendritic cells and alveolar macrophages are believed to capture viral particles in the lungs allowing spread via infected cells. This is known as a Trojan horse entry mechanism like that used by HIV to pass through mucosal tissues and infect humans – see below. This infection allows for spread and localised replication within nearby lymphoid tissues and then on to draining lymph nodes where massive lymphocyte cell infection may occur facilitating dissemination throughout the host, mainly within lymphoid tissues. Virus can be carried through host blood vessels to other lymphoid target tissues like the tonsils and adenoids and the gut-associated lymphoid tissue ‘ Peyer’s patches’.

HIV entry mechanisms utilising dendritic cells to pass through epithelial cell barriers - the 'Trojan horse' mechanism. This may be directly analogous to MeV entry and primary spread except in the respiratory tract.

What does this mean?

This study clearly demonstrates the importance of non-epithelial cells such as dendritic cells in MeV entry, early replication and subsequent systemic spread. It does not however, rule out a major role for epithelial cells in later stages and in transmission – MeV still infects non-CD150 expressing cells and currently the mechanisms of which are unknown. Focusing on the later stages of infection may allow us to appreciate the other cell targets in pathogenesis and viral transmission. As mentioned previously, the use of fluorescent-labeled viruses offers an unprecedented view of viral entry, spread and pathogenic mechanisms. We should look forward to the time when studies like these are applied to other viral and indeed non-viral pathogens.

ResearchBlogging.orgLemon, K., de Vries, R., Mesman, A., McQuaid, S., van Amerongen, G., Yüksel, S., Ludlow, M., Rennick, L., Kuiken, T., Rima, B., Geijtenbeek, T., Osterhaus, A., Duprex, W., & de Swart, R. (2011). Early Target Cells of Measles Virus after Aerosol Infection of Non-Human Primates PLoS Pathogens, 7 (1) DOI: 10.1371/journal.ppat.1001263

Coombes, J., & Robey, E. (2010). Dynamic imaging of host–pathogen interactions in vivo Nature Reviews Immunology, 10 (5), 353-364 DOI: 10.1038/nri2746

Written by Connor

February 1, 2011 at 11:06 am

A Mouse Model of XMRV Pathogenesis?

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Through studying viral pathogenesis we seek to understand mechanistically how viral infection and replication causes disease in a particular host. This of course will be subject to a number of complex variables involving both the host and the virus such as: dose; genotype; virus receptor distribution of host tissues;the ability of the virus to replicate in those infected cells and the hosts response to that infection.

Although it is an extremely complex system, knowledge of it may allow us to develop certain preventative strategies alongside new treatments and therapies. That is why being able to study viral pathogenesis is important and why some may welcome a recently published paper reporting initial data (possible cell tropism and host immune response) from a mouse model of infection with xenotropic murine leukemia-related virus (XMRV), a possible novel human pathogen (and a close relation of natural mouse retroviruses).

Mus musculus - relative of Mus pahari. Just incase you forgot what a mouse looked like.

Originally identified in a number of human prostate tumour samples, XMRV has since had a conflicting scientific history (covered much better elsewhere), with some studies showing a link between infection and chronic fatigue syndrome (CFS) and prostate cancer. Others since have failed to detect such a link. Despite this, knowledge of how this virus could potentially interact with the human body would of course be useful to acquire.

This understanding has been blocked somewhat by the lack of a small-animal model – a cheap, easier and more ethical alternative to non-human primate studies and of course easier to study than humans. XMRV just does not infect normal lab mice (Mus musculus) and thus pathogenesis in this host does not occur and if pathogenesis doesn’t occur, we can’t study pathogenesis. This species of mouse doesn’t express the receptor that XMRV utilizes to gain entry into cells. Sakuma et al have therefore used Mus pahari, a wild asian relative which does express the receptor for XMRV and thus may tell us something about XMRV pathogenesis.

The group showed that XMRV was able to successfully infect M. pahari cells in vitro and also was able to infect M. pahari following injection of the virus into whole-animals. Following infection, they were able to screen mouse cells and tissues (such as blood) for the telltale signs of XMRV infection over 12 weeks; XMRV being a retrovirus, integrates a DNA copy of its RNA genome into host cells and PCR detection of this integration may allow us to infer XMRV infection. They also investigated the possible role of infectious virus being present in the animal and the of XMRV replication on host cell functioning.

Detection of XMRV DNA in particular tissues may allow us to infer how infection proceeds within the host and how it causes disease. Viral sequences were detected in blood cells, heart, spleen, brain, testis and prostate tissues, although detection was highly variable between mice and a clear picture of infection didn’t really emerge over any of the time periods. The group focused on the effect of XMRV on lymphocytic cell functioning (possibly a good place to start giving its apparent involvement in CFS, an immunological disorder): CD4+ T helper cells and CD19+ B cells being targeted within the spleen. Over all, in some of the mice, increased total white-blood cell numbers was observed early in infection indicating a possible deregulation of lymphocyte development, although this was by no means common and only slight.

The role of both mouse adaptive and innate immunity was also assessed and interestingly, the mice generated a robust antibody response to XMRV antigens yet no long-term studies were involved to see how the virus adapted. Viral genome sequences found within blood and spleen tissues were sequenced and those from the spleen only, displayed predominant G-to-A hypermutation possibly indicative of intra-tissue restriction of viral replication. Host-mediated mutation of viral genomes will therefore more likely result in highly defective viral sequences and possibly prevent future viral infections; one example is that of APOBEC3-like enzymatic reactions.

Of course, these data are rather preliminary with optimisation of infection expected to come later, but at the minute, how does this relate to what happens in humans and will this model actually be on any use?

  • The development of a permissive small-mammal model of XMRV infection described here will certainly facilitate scientific investigation as it has done for many other viruses although it must be remembered that what happens in a mouse may not happen exactly that way in humans.
  • This study, however does appear to shed light on cell tropism of XMRV and possibly its transmission – blood-borne (although this was looked at really).
  • The possible deregulation of host lymphocyte development may play a role in the pathologies associated with it in humans. The highly variable pathological outcomes may be due to the relatively less homogenous gene pool of M. pahari rather than anything to do with the virus – although this may be occurring.
  • The fact that these mice developed strong antibody responses to this virus may allow the development of vaccine strategies.

But, of course, the importance and relevance of this work will all come down to whether it is or is not a true human pathogen yet we will certainly benefit from this work if it turns out that it is. Expect a lot more from this group if it is.

Sakuma T, Tonne JM, Squillace KA, Ohmine S, Thatava T, Peng KW, Barry MA, & Ikeda Y (2011). Early Events in Retrovirus XMRV Infection of the Wild-Derived Mouse Mus pahari. Journal of virology, 85 (3), 1205-13 PMID: 21084477

Sakuma T, Tonne JM, Squillace KA, Ohmine S, Thatava T, Peng KW, Barry MA, & Ikeda Y (2011). Early Events in Retrovirus XMRV Infection of the Wild-Derived Mouse Mus pahari. Journal of virology, 85 (3), 1205-13 PMID: 21084477

Written by Connor

January 26, 2011 at 8:46 pm

Seeing the big picture of RNA virus evolution

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This post was chosen as an Editor's Selection for

From both a medical and a scientific viewpoint, the evolution of viruses is extremely important to us;  viral adaptation to their ever changing environment is responsible for major morbidity and mortality worldwide so maybe studying this  may allow us to predict virus evolution in the future and may help prevent pandemics occuring?

We kind of know a lot about how viruses evolve at the small-scale; we know how viruses generally create genetic diversity – mutations – and how processes such as natural selection and genetic drift act on these genetic changes and influence the way viral genomes change over time. What we don’t know however, is how viruses change at the larger-scale – how these above processes influence viral genomes over thousands of years, including: how and why viruses speciate, how their genome structure evolves and how and when do new viruses originate.

An example phylogenetic tree - The paramyxoviridae containing a number of important human and animal pathogens. Notice the host/viral species distribution.

A recent study, investigating the evolution of a number of RNA viruses has sought to reconcile this lack of understanding by attempting to assess virus ‘macroevolution’- specifically viral speciation. By generating large and highly robust phylogenetic trees (using significantly highly conserved amino-acid sequences of a single viral protein) for 5 genera of RNA virus including: the Alphaviruses, Caliciviruses, Paramyxoviruses, Rhabdoviruses and the Flaviviruses, the team were able to map the host species of each virus species onto the trees and this allowed them to infer the mode of speciation of each virus genus.

More specifically they asked: Do closely related viral species infect the same host and are therefore believed to have speciated in that host or do they infect completely different hosts which are believed to have speciated following host jumping?

What is a virus species?

General modes of speciation - we may think of viruses speciating by either allopatric (host shift) or sympatric (intra-host divergence).

The concept of the viral species has been a hard one to determine becuase viruses don’t reproduce sexually. It is generally thought to be rather a arbitrary classification, however, most virus ‘species’ tend to be phylogenetically and often phenotypically stable genetic lineages and hence may be thought of as ‘biological relevant’. We may think of viral speciation much like we think of speciation in the classic sense: allopatric or ‘geographical speciation’ (virus adaptation to a new host species) and sympatric – that not requiring the forces of georgaphic isolation (generation of viral speciation within a single host). Virus sympatric speciation requires the adapation to a new infectious niche within a host, for example a new lineage may infect new cell types within that host. Virus allopatric speciation requires host-jumping or adaptation to a new host altogether but may result from co-divergence follwoing host speciation. Both processes may result in two or more ‘stable, phylogenetic and phenotypic genetic lineages. But what does the data say about it – how do viruses evolve in the real world?

What the data says

The results were split – at leats 50% were found to have ‘speciated’ via sympatric-like processes and half from allopatric-like processes. The group stress, however, that a major caveat of this study is that it highlights our limited understanding of what specific host speces particular viruses infect; in this study most hosts were classified as ‘birds’ or ‘plants’ or ‘Carnivores’ which limits the resolution of phylogenetic studies and leads to the overestimation of sympatric speciation events which would otherwise not exist if exact hosts were known. This leads us to put little confidence on our earlier 50/50 estimate and most likely the role of sympatric speciation would be a lot less important than allopatric modes of speciation in reality.

Why do RNA viruses evolve this way – What controls viral speciation?

So, we may say that most RNA virus speciation is caused by allopatric modes – or host jumping, but this may seem counterintuitive as there are some major barriers to viral emergence. The group argue, however, that it may take a lot more – genetically speaking – for a virus to speciate within a host than it does for a virus to jump species – eg. replicate in a new cell type/alter antigenic epitopes. The apparant preference for allopatric speciation may be controlled by intrinsic biological factors of these RNA viruses, namely: their extremely small genome size which effectively constrains evolutionary innovation. Those changes required for host jumping (change in receptor binding sites for instance) may be relatively minor when compared to those and the more closely related the host species are then the more easily host-jumping will occur – which is what we see here.

This study highlights the key role that viral ‘allopatric’ speciation or host – jumping plays in the evolution of RNA viruses yet further emphasizes the need to better study and understand viral biodiversity and host range in the wild – not only focusing on those medically important human viruses. Further research may be carried out on the molecular barriers to both cellular and host switching for these RNA viruses. This study will act as a model system that may be applied to other viral lineages – what about the RNA viruses with segmented genomes? What about the DNA viruses? Retroviruses?
Kitchen A, Shackelton LA, & Holmes EC (2011). Family level phylogenies reveal modes of macroevolution in RNA viruses. Proceedings of the National Academy of Sciences of the United States of America, 108 (1), 238-43 PMID: 21173251

Written by Connor

January 17, 2011 at 1:25 pm

Measles, Papua New Guinea and the brain

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This post was chosen as an Editor's Selection for ResearchBlogging.orgYou may not have realised that – since most people nowadays have been vaccinated against it and have never seen it – but measles is a very serious illness. Generally an acute disease of children, measles is spread by the measles virus where it infects the body via the respiratory route and establishes a systemic infection – involving multiple organ systems – via your bodies own immune cells leading to the typical rash, mild to severe respiratory distress and immunosuppression (Rima and Duprex 2006).

Measles virus replicative cycle

In the ‘developed’ world we tend not to think about infectious disease in the same way as people in other parts of the world; national vaccination campaigns have largely removed the threat (not considering some minor outbreaks) of the some of the biggest human killers and we no longer worry ourselves over whether a family member will come down with these diseases.

Subacute Sclerosing Panencephalitis or SSPE is one of the most serious complications of measles resulting from viral infection of the central nervous system; SSPE is rare (1 in 10,000-25,000 measles infections) but is almost always fatal. Following infection at a particularly young age and on average 8 years following acute infection, a progressive deterioration of neurological function presents : loss of attention span, uncontrolled movements, behavioural changes, cognitive impairment and in all cases vegetative state is entered and death occurs.

It is caused by persistent measles infection i.e one that the isn’t removed when your immune system kicks in, which spreads throughout the  cells found within the brain causing cell death and inflammation. Strangely, no infectious virus can be recovered from infected brains and when this was investigated further they found that many mutations occurred throughout the genome rendering many of the genes nonfunctional. Although the major replicative functions (replication and gene expression) were left intact, the genes required for normal particles formation were those mutated suggesting that the virus may exploit the unique cellular environment in the CNS to spread, replicate and survive.

Green Fluorescent Protein expressing measles virus infection of neuronal cell

As I mentioned previously, due to increased transmission of virus, poverty and poor nutrition, measles infection is extremely serious in developing countries and it is no surprise that SSPE occurs here in higher numbers. In Papua New Guinea there exists a very high incidence of SSPE, THE highest incidence – roughly 3 – 20 times as many cases are reported (98 per million people versus 5 per million people). Manning et al (2011) have attempted to further characterise SSPE behaviour in this country between 1997 and 2008 and highlights the significant burden that measles is in many developing countries. They measured SSPE incidence, measles infection rates and time of birth of each patient presenting with SSPE finding a direct correlation between time of birth, measles epidemics and presenting with SSPE. The group emphasises the requirement

Why is SSPE incidence so high here and what can we do about it? SSPE rates are linked to measles infections in a population and hence have been significantly reduced following measles vaccination campaigns. Sadly, only half of children in Papua New Guinea receive two measles vaccines prior to 1st birthday – not enough to sufficiently protect an individual nor a population from measles infection and hence SSPE; there is insufficiently low-level of herd immunity in regions such as papua New Guinea. The level of vaccine effectiveness of measles vaccine in this region is also particularly low – possibly reflecting damage to the vaccine from cold-chain disruption (in tropical climates it is difficult to keep vaccines refrigerated), population genetic effects or persistence of low-level non-neutralising maternal antibody.

We can no longer afford to ignore the importance of measles in developing countries like Papua New Guinea and we must stress the need for adequate vaccine effectiveness and coverage in already susceptible human populations. Studies like these with SSPE emphasise the real-world need for the investigation of the molecular mechanisms of measles virus persistence and we should look forward to a time when we can adequatly treat measles CNS complications – or maybe with better vaccination coverage we may not have to worry about this.

Manning, L., Laman, M., Edoni, H., Mueller, I., Karunajeewa, H., Smith, D., Hwaiwhanje, I., Siba, P., & Davis, T. (2011). Subacute Sclerosing Panencephalitis in Papua New Guinean Children: The Cost of Continuing Inadequate Measles Vaccine Coverage PLoS Neglected Tropical Diseases, 5 (1) DOI: 10.1371/journal.pntd.0000932

Rima, B., & Duprex, W. (2006). Morbilliviruses and human disease The Journal of Pathology, 208 (2), 199-214 DOI: 10.1002/path.1873

Written by Connor

January 10, 2011 at 8:50 pm

Posted in Measles, Vaccines

Tagged with , ,