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Seeing the big picture of RNA virus evolution

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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

Massively parallel sequencing meets the vaccine industry

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Live attenuated vaccines (LAVS), such as those produced for measles, mumps and influenza viruses, must have both high safety and immunogenicity if we are ever going to prevent human infection. Those vaccines, which are deemed unsafe, will be withdrawn resulting in low uptake and increased pathogen transmission and those vaccines which are poorly immunogenic, will not be  protective and result in pathogen transmission and significant disease

The key to easily predicting how safe a vaccine is – and also how immunogenic -, may lie in our ability to infer the phenotype (safety in humans) from the genotype (nucleic acid sequence). One problem with this is the inherent genetic instability of  RNA viruses; viruses such as polio, measles and mumps which are responsible for considerable disease in humans and which we vaccinate millions of people worldwide each year. This genetic instability results in what is generally considered as a viral ‘qausipecies’; a cloud-like structure in viral genome sequence space that can have multiple phenotypic properties: one being the safety, or lack of in humans. One example is that of oral polio vaccine strains which during production in tissue culture can accumulate genomic changes resulting in neurovirulence in humans.

In order to assess the safety we must therefore assay the genetic consistency or the types and frequency of particular changes in our vaccines prior to human administration to avoid vaccine induced disease. As I mentioned previously, our ability to assess the safety relies on our means of predicting phenotype from genotype, something that for most viruses is particularly difficult and time consuming. We are therefore  in a position in which we do not know the genetic determinants of safety and so cannot predict it based on nucleic acid sequence.

MPS analysis of two batches of type 3 OPV performed by pyrosequencing. (A) The number of times each nucleotide was read in forward (green) and reverse (red) orientations. (B and C) Mutational profiles for vaccine batches that failed and passed the MNVT, respectively. Here and in all other figures the contents of mutants is shown by colored bars: mutations to A shown in orange, mutations to C in red, mutations to G in blue, and mutations to U in green. Neverov & Chumakov.(2010)

Neverov and Chumakov, from the American Food and Drug association (FDA) recently published a method in which massively parallel sequencing (MPS) is used to accurately and rapidly quantify nucleotide changes across entire poliovirus vaccine genomes.  This method proved to be very sensitive at detecting low frequency changes, changes that may have led to disease in humans. The group put forward the view that we do not truly have to know the direct relationship between genome sequence and safety but what we can do is compare the genotype and frequency of each change with previous ‘safe’ vaccine sequences. Vaccines will be allowed for human use if they have similar viral populations as a previously used strain. They offer this method as a replacement to the slower and less accurate mutant analysis by PCR and restriction enzyme cleavage (MAPREC) method.

The authors admit that the wide-scale implementation of MPS will be inhibited by the high running cost of the equipment.; a cost that they say is much less than the previously used primate neuroviruelance assay. Investment in this technology is expected to lead to a rapid decrease in price and hence will result in increased uptake of this in LAV production worldwide. Neverov and Chumakov have applied this novel sequencing technology to an important area of the vaccine industry. This application will find use in not only polio vaccines but in other LAV production and may also be implemented in the discovery of new genetic determinants of viral safety and immunogenicity.

Neverov, Alexander, and Konstantin Chumakov. 2010. Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines. Proceedings of the National Academy of Sciences of the United States of America 107, no. 46 (November). doi:10.1073

Written by Connor

December 23, 2010 at 7:23 pm