T cell exhaustion during persistent viral infections

Why does the immune system fail to clear some virus (and other infections) and allow a state of chronic infection to occur? And when it does, how are immune responses different from a non-infected individual? This article describes the processes involved in T cell exhaustion and considers what can be done to reconstitute the immune system in chronic infections, including HIV.

T cell exhaustion during persistent viral infections

T cell exhaustion during persistent viral infections. (2015) Virology. 22 Jan. doi: 10.1016/j.virol.2014.12.033
Although robust and highly effective anti-viral T cells contribute to the clearance of many acute infections, viral persistence is associated with the development of functionally inferior, exhausted, T cell responses. Exhaustion develops in a step-wise and progressive manner, ranges in severity, and can culminate in the deletion of the anti-viral T cells. This disarming of the response is consequential as it compromises viral control and potentially serves to dampen immune-mediated damage. Exhausted T cells are unable to elaborate typical anti-viral effector functions. They are characterized by the sustained upregulation of inhibitory receptors and display a gene expression profile that distinguishes them from prototypic effector and memory T cell populations. In this review we discuss the properties of exhausted T cells; the virological and immunological conditions that favor their development; the cellular and molecular signals that sustain the exhausted state; and strategies for preventing and reversing exhaustion to favor viral control.

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Life in Our Phage World

Life in Our Phage World In 1915 Frederick Twort made the first scientific observations on bacteriophages (followed shortly after by Félix d’Herelle). In the century that has followed, phage research has revolutionized our understanding of biology.

“[the] molecular biology of higher organisms does not stand on the shoulder of giants, but on the shoulder of dwarfs like phage T4 and lambda.”
Harald Brüssow

Phage and other viruses outnumber all other organic entities on our planet, with an estimated numbers at a mind-boggling 1031. To celebrate 100 years of phage research, a conference was held in San Diego in January and all the contributions were captured on the 2015 year of the Phage website. This includes a 400 page book which describes in detail 30 diverse phages, including, where on Earth they’ve been found, who their close relatives are, how their genomes are structured, and how they trick their hosts into submission. Researchers who have devoted their lives to phage also recount their experiences. You can download a free copy of the book from the website, and it’s well worth reading.

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HIV Rev – Really Exasperating Virus protein

HIV Rev When viruses infect cells, they often use specialized proteins that hijack the host cell’s proteins to carry out essential tasks. For example, human immunodeficiency virus (HIV) needs to transport copies of its RNA out of the nucleus of the host cell and into the cell’s cytoplasm in order to create important viral proteins. To do this, a protein in HIV called Rev hijacks a transporter protein that carries cargo across the membrane that surrounds the cell nucleus. As a biochemical entity, Rev has proven to be truly exasperating over the last two miserable decades due to its propensity to generally misbehave – by aggregating or forming fibrils or oligomers – when studied in the laboratory. Now, in eLife, two papers provide a more detailed structural picture of how Rev works.

eLife: Really exasperating viral protein from HIV

Related articles:

RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex. (2014) eLife 3: e04120. doi: 10.7554/eLife.04120

The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA. (2014) eLife 3: e04121. doi: 10.7554/eLife.04121

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Paramyxovirus polymerase: transcription or replication?

Paramyxovirus polymerase -   transcription or replication

The paramyxovirus family has a genome consisting of a single strand of negative sense RNA. This genome acts as a template for two distinct processes: transcription to generate subgenomic, capped and polyadenylated mRNAs, and genome replication. These viruses only encode one polymerase. Thus, an intriguing question is, how does the viral polymerase initiate and become committed to either transcription or replication? By answering this we can begin to understand how these two processes are regulated.

This review article presents recent findings from studies on the paramyxovirus, respiratory syncytial virus, which show how its polymerase is able to initiate transcription and replication from a single promoter and discusses how these findings apply to other paramyxoviruses. It also examines how trans-acting proteins and promoter secondary structure might serve to regulate transcription and replication during different phases of the paramyxovirus replication cycle.

Initiation and regulation of paramyxovirus transcription and replication. Virology. 12 Feb 2015 doi: 10.1016/j.virol.2015.01.014

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Coronavirus Cell Entry Requires Proteolysis of the S Protein

Coronavirus Cell Entry Requires Proteolysis of the S Protein Enveloped viruses need to fuse with a host cell membrane in order to deliver their genome into the host cell. CoVs are important pathogens of animals and man with high zoonotic potential as demonstrated by the emergence of SARS- and MERS-CoVs. A recent study investigated the cell entry of coronaviruses (CoVs).

Previous studies resulted in apparently conflicting results with respect to CoV cell entry, particularly regarding the fusion-activating requirements of the CoV S protein. By combining cell-biological, infection, and fusion assays the authors demonstrated that murine hepatitis virus (MHV), a prototypic member of the CoV family, enters cells via clathrin-mediated endocytosis. Moreover, although MHV does not depend on a low pH for fusion, the virus was shown to rely on trafficking to lysosomes for proteolytic cleavage of its spike (S) protein and membrane fusion to occur.

Based on these results they predicted and then demonstrated that MERS- and feline CoV require cleavage by different proteases and escape the endo/lysosomal system from different compartments.

Coronavirus Cell Entry Occurs through the Endo-/Lysosomal Pathway in a Proteolysis-Dependent Manner. (2014) PLoS Pathog 10(11): e1004502. doi: 10.1371/journal.ppat.1004502

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Poliovirus replication – many generations per cell

Poliovirus replication Viruses with RNA genomes can multiply quickly, but not very accurately. This means that errors, or mutations, occur when the RNA is copied to create new viruses. The advantage of this rapid, but mistake-filled, RNA replication process is that some of the mutations will be beneficial to the virus. This allows viruses to rapidly evolve, for example, to develop resistance against drugs.

Poliovirus is an RNA virus that can cause paralysis and death in humans. To prevent such infections, scientists have extensively studied the poliovirus and have developed effective vaccines against it that have eliminated the virus from all but a few countries. Because so much is known about the poliovirus and because it has a very simple structure, scientists continue to use the poliovirus as a model to study virus behavior.

One unknown aspect of the poliovirus’ behavior is how it replicates after invading a cell. Are all of its RNA copies made from the original viral RNA that first infected the cell, in what is known as a ‘stamping machine’ model? Or do the new copies of the RNA also get copied themselves in a ‘geometric replication mode’ that increases the likelihood of mutations and enables the virus to evolve more rapidly?

Viral RNA molecules are copied by one of the virus’s own proteins and so before the viral RNA can be replicated, it must first be translated to form viral proteins. When and where replication begins depends on the concentration of translated proteins around the RNA and so replication tends to begin in particular areas of the cell at different times. A recent paper used mathematical modeling to create computer simulations of the number of polioviruses in a cell that take into account these time and space constraints. By including random elements in the model, the simulated behavior more accurately follows experimentally recorded data than previously used models.

The results of the model led the authors to conclude that the poliovirus replicates by the ‘geometric mode'; as new copies of the poliovirus RNA are made, each copy goes on to make more copies. This means that in a single infected cell there are multiple generations of RNA, and each generation may undergo distinct mutations that are passed on to the next set of RNA copies. In fact, the average virus released from an infected cell is the great-great-great-granddaughter of the original virus that infected the cell. With so many different generations of virus coexisting in a cell, there are a lot of opportunities for new genetic combinations to occur and for viruses to evolve new abilities.

Experimentally guided models reveal replication principles that shape the mutation distribution of RNA viruses. (2015) eLife 4: e03753 doi: 10.7554/eLife.03753
Life history theory posits that the sequence and timing of events in an organism’s lifespan are fine-tuned by evolution to maximize the production of viable offspring. In a virus, a life history strategy is largely manifested in its replication mode. Here, we develop a stochastic mathematical model to infer the replication mode shaping the structure and mutation distribution of a poliovirus population in an intact single infected cell. We measure production of RNA and poliovirus particles through the infection cycle, and use these data to infer the parameters of our model. We find that on average the viral progeny produced from each cell are approximately five generations removed from the infecting virus. Multiple generations within a single cell infection provide opportunities for significant accumulation of mutations per viral genome and for intracellular selection.

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The arthropod origins of RNA viruses

Negative sense RNA viruses in arthropods and non-arthropods A new paper in eLife describes the genetic diversity and novel genome structures of RNA viruses from arthopods, shedding new light on the ancestry and evolutionary history of plant and animal RNA viruses.


Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. eLife January 29 2015; doi: 10.7554/eLife.05378
Although arthropods are important viral vectors, the biodiversity of arthropod viruses, as well as the role that arthropods have played in viral origins and evolution, is unclear. Through RNA sequencing of 70 arthropod species we discovered 112 novel viruses that appear to be ancestral to much of the documented genetic diversity of negative-sense RNA viruses, a number of which are also present as endogenous genomic copies. With this greatly enriched diversity we revealed that arthropods contain viruses that fall basal to major virus groups, including the vertebrate-specific arenaviruses, filoviruses, hantaviruses, influenza viruses, lyssaviruses, and paramyxoviruses. We similarly documented a remarkable diversity of genome structures in arthropod viruses, including a putative circular form, that sheds new light on the evolution of genome organization. Hence, arthropods are a major reservoir of viral genetic diversity and have likely been central to viral evolution.

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Understanding Ebola Virus Transmission

The 2014 outbreak of Ebola virus disease in West Africa has claimed more lives than all previous Ebola outbreaks combined. Along with its high case fatality rate, this outbreak has caused infection of several local and foreign health care workers. In order to understand outbreak control and determine appropriate public health practices, as well as guide future avenues of research, it is important to assess the current state of our knowledge about Ebola virus transmission between people.

This short review describes different routes of Ebola virus transmission between people, summarizing the known epidemiological and experimental data.

Ebola Virus Transmission

Understanding Ebola Virus Transmission. (2015) Viruses, 7(2): 511-521; doi: 10.3390/v7020511
An unprecedented number of Ebola virus infections among healthcare workers and patients have raised questions about our understanding of Ebola virus transmission. Here, we explore different routes of Ebola virus transmission between people, summarizing the known epidemiological and experimental data. From this data, we expose important gaps in Ebola virus research pertinent to outbreak situations. We further propose experiments and methods of data collection that will enable scientists to fill these voids in our knowledge about the transmission of Ebola virus.

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Polintons and network-like evolution of the virus world

Polintons Eukaryote genomes are populated by DNA copies of parasitic elements known as transposable elements capable of reproducing themselves in the host genome in a non-Mendelian fashion. Understanding the biology of transposable elements is important because of their impact on genome evolution. Eukaryotic transposable elements were thought to belong to only two types, called retrotransposons and DNA transposons. Retrotransposons are replicated via reverse transcription of its mRNAs, DNA transposons are transposed via transfer of its genomic copy from one site to another. In 2005, a new class of transposable element was proposed, the Polintons:

Self-synthesizing DNA transposons in eukaryotes. (2006) Proceedings of the National Academy of Sciences of the United States of America, 103(12): 4540-4545
Eukaryotes contain numerous transposable or mobile elements capable of parasite-like proliferation in the host genome. All known transposable elements in eukaryotes belong to two types: retrotransposons and DNA transposons. Here we report a previously uncharacterized class of DNA transposons called Polintons that populate genomes of protists, fungi, and animals, including entamoeba, soybean rust, hydra, sea anemone, nematodes, fruit flies, beetle, sea urchin, sea squirt, fish, lizard, frog, and chicken. Polintons from all these species are characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. In addition, Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5′-AG and TC-3′ termini. Analogously to known transposable elements, Polintons exist as autonomous and nonautonomous elements. Our data suggest that Polintons have evolved from a linear plasmid that acquired a retroviral integrase at least 1 billion years ago. According to the model of Polinton transposition proposed here, a Polinton DNA molecule excised from the genome serves as a template for extrachromosomal synthesis of its double-stranded DNA copy by the Polinton-encoded DNA polymerase and is inserted back into genome by its integrase.

A new review article looks at the relationship between Polintons and viruses and suggests that that Polintons were the first group of eukaryotic double-stranded DNA viruses to evolve from bacteriophages and that they gave rise to most large DNA viruses of eukaryotes and various other selfish genetic elements:

Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution. (2015) Nature Reviews Microbiology 13: 105–115 doi:10.1038/nrmicro3389
Polintons (also known as Mavericks) are large DNA transposons that are widespread in the genomes of eukaryotes. We have recently shown that Polintons encode virus capsid proteins, which suggests that these transposons might form virions, at least under some conditions. In this Opinion article, we delineate the evolutionary relationships among bacterial tectiviruses, Polintons, adenoviruses, virophages, large and giant DNA viruses of eukaryotes of the proposed order ‘Megavirales’, and linear mitochondrial and cytoplasmic plasmids. We hypothesize that Polintons were the first group of eukaryotic double-stranded DNA viruses to evolve from bacteriophages and that they gave rise to most large DNA viruses of eukaryotes and various other selfish genetic elements.


Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies. (2013) Virol J, 10(158): doi: 10.1186/1743-422X-10-158
Recent advances of genomics and metagenomics reveal remarkable diversity of viruses and other selfish genetic elements. In particular, giant viruses have been shown to possess their own mobilomes that include virophages, small viruses that parasitize on giant viruses of the Mimiviridae family, and transpovirons, distinct linear plasmids. One of the virophages known as the Mavirus, a parasite of the giant Cafeteria roenbergensis virus, shares several genes with large eukaryotic self-replicating transposon of the Polinton (Maverick) family, and it has been proposed that the polintons evolved from a Mavirus-like ancestor. We performed a comprehensive phylogenomic analysis of the available genomes of virophages and traced the evolutionary connections between the virophages and other selfish genetic elements. The comparison of the gene composition and genome organization of the virophages reveals 6 conserved, core genes that are organized in partially conserved arrays. Phylogenetic analysis of those core virophage genes, for which a sufficient diversity of homologs outside the virophages was detected, including the maturation protease and the packaging ATPase, supports the monophyly of the virophages. The results of this analysis appear incompatible with the origin of polintons from a Mavirus-like agent but rather suggest that Mavirus evolved through recombination between a polinton and an unknown virus. Altogether, virophages, polintons, a distinct Tetrahymena transposable element Tlr1, transpovirons, adenoviruses, and some bacteriophages form a network of evolutionary relationships that is held together by overlapping sets of shared genes and appears to represent a distinct module in the vast total network of viruses and mobile elements. The results of the phylogenomic analysis of the virophages and related genetic elements are compatible with the concept of network-like evolution of the virus world and emphasize multiple evolutionary connections between bona fide viruses and other classes of capsid-less mobile elements.

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