Can we prevent norovirus infections?

Norovirus Each year, noroviruses cause over 200,000 deaths and a global economic burden of US$64 billion. A highly contagious virus that most people will contract 5 times in their lifetime, the most serious outcomes of the disease – hospitalization and death – are far more common among children and the elderly, and in low and middle income countries. In a new PLOS Collection – The Global Burden of Norovirus & Prospects for Vaccine Development – global norovirus experts fill critical knowledge gaps and provide key information to further development of a much-needed vaccine:

  • The Vast and Varied Global Burden of Norovirus: Prospects for Prevention and Control
  • Global Economic Burden of Norovirus Gastroenteritis
  • Norovirus Epidemiology in Africa: A Review
  • Population-Based Incidence Rates of Diarrheal Disease Associated with Norovirus, Sapovirus, and Astrovirus in Kenya
  • Incidence of Norovirus and Other Viral Pathogens That Cause Acute Gastroenteritis (AGE) among Kaiser Permanente Member Populations in the United States, 2012–2013
  • Incidence of Norovirus-Associated Medical Encounters among Active Duty United States Military Personnel and Their Dependents
  • Early Detection of Epidemic GII-4 Norovirus Strains in UK and Malawi: Role of Surveillance of Sporadic Acute Gastroenteritis in Anticipating Global Epidemics
  • Norovirus Recombinant Strains Isolated from Gastroenteritis Outbreaks in Southern Brazil, 2004–2011
  • A Multi-Site Study of Norovirus Molecular Epidemiology in Australia and New Zealand, 2013-2014
  • Vomiting as a Symptom and Transmission Risk in Norovirus Illness: Evidence from Human Challenge Studies
  • Correlates of Protection against Norovirus Infection and Disease—Where Are We Now, Where Do We Go?
  • Innate Resistance and Susceptibility to Norovirus Infection
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How immunity to RSV develops in childhood but deteriorates in adults

Respiratory Syncytial Virus A leading infectious cause of severe respiratory disease in infants, respiratory syncytial virus (RSV), is also a major cause of respiratory illness in the elderly. Approved vaccines do not yet exist, and despite the development of partial immunity following infection during childhood, individuals remain susceptible to RSV reinfection life-long.

RSV is nearly ubiquitous, and most children are born with some protective immunity conveyed by maternal antibodies. As the maternal antibodies wane over time, infants become susceptible, and are often infected for the first time between nine months and two years of age. Studies over the past three decades have explored the antibody responses before and after RSV infection in different age groups. We know that human antibodies that can mediate the destruction (or neutralization) of the virus target the two major proteins on the virus surface, namely the attachment protein G and the fusion protein F. However, which antibody combination conveys the best immune protection, and why RSV infections recur throughout life remain open questions. This study of the antibody-response to RSV advances our understanding of the human immune response against RSV and has implications for vaccine design.

The blood of young infants contains maternal antibodies that recognize several parts of both the F and G proteins. In older infants that had been infected with RSV, they saw a dramatic expansion in both quantity and diversity of the antibodies that recognized the G protein. Surprisingly, infection prompted only a modest increase in the antibody repertoire against the F protein. Looking at changes over time, the researchers found that the antibodies against the F protein continued to expand with age whereas those against the G protein weakened. Because the G protein sequence varies between RSV strains, whereas the F protein is highly conserved among strains, some vaccines under development use only the more tractable F protein as a vaccine antigen. The results suggest that such a vaccine design might be problematic. On the other hand, the fact that the strong anti-G responses seen in children target a relatively conserved region in the G protein suggest that variability in other parts of the G protein does not necessarily compromise G’s utility as a vaccine antigen.

 

Antigenic Fingerprinting following Primary RSV Infection in Young Children Identifies Novel Antigenic Sites and Reveals Unlinked Evolution of Human Antibody Repertoires to Fusion and Attachment Glycoproteins. (2016) PLoS Pathog 12(4): e1005554. doi:10.1371/journal.ppat.1005554
Respiratory syncytial virus (RSV) is the major cause of pneumonia and bronchiolitis among infants and children globally. In the United States, RSV infections lead to 57,000 hospitalizations among young children, especially in those less than one year old. Further- more, despite the development of immunity following RSV infection during childhood, individuals remain susceptible to RSV upper respiratory tract reinfection. In the current study we explored the antibody repertoires following primary RSV infection and their evo- lution in adolescents and adults. Whole genome-fragment phage display libraries (GFPDL) expressing linear and conformational epitopes from RSV fusion protein (F) and attachment protein (G) were used for unbiased epitope profiling of sera prior to and fol- lowing RSV infection. In addition, Plasmon Surface Resonance (SPR) was used to measure antibody binding to F and G peptides and proteins. A steady increase in RSV-F epitope repertoires from young children to adults was observed. Several novel epitopes were iden- tified in pre-fusion F and an immunodominant epitope in F0-p27. For RSV-G, antibody responses were high following RSV infection in children, but declined in adults. This study identified unlinked evolution of anti-F and anti G responses that could help development of better RSV vaccines and therapies.

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The parasite’s new clothes

Schistosome surface Schistosomes are a type of parasitic flatworm, or fluke, and inhabit a site in the human body that is inhospitable to most other parasites – the blood. Yet instead of succumbing to our immune cells, the flukes can dwell in the bloodstream for many years. The fluke’s outer surface, or tegument, is key to its success as a long-lived parasite. The tegument clothes the entire adult fluke and hides its most vulnerable tissues from the prying eyes of the immune system. As such, it is us as human hosts (and not the flukes) who are fooled by the parasites’ remarkable “clothes”.

A fluke’s tegument forms an almost impenetrable barrier between the parasite and its host. It also orchestrates an array of processes that allow the fluke to go about its parasitic lifestyle. Many researchers consider the tegument as a rich source of molecules that could be targeted by vaccines and drugs to combat schistosomiasis. Recent studies have revealed a great deal about the molecular composition of the tegument, but we know far less about how the tegument regenerates after it has been damaged Now in eLife, researchers tell a previously untold chapter in this tale of parasitic flatworms – how a population of stem cells continuously rejuvenates the outer surface of a human parasitic flatworm.

 

Stem cell progeny contribute to the schistosome host-parasite interface. (2016) eLife 5: e12473 doi: 10.7554/eLife.12473
Schistosomes infect more than 200 million of the world’s poorest people. These parasites live in the vasculature, producing eggs that spur a variety of chronic, potentially life-threatening, pathologies exacerbated by the long lifespan of schistosomes, that can thrive in the host for decades. How schistosomes maintain their longevity in this immunologically hostile environment is unknown. Here, we demonstrate that somatic stem cells in Schistosoma mansoni are biased towards generating a population of cells expressing factors associated exclusively with the schistosome host-parasite interface, a structure called the tegument. We show cells expressing these tegumental factors are short-lived and rapidly turned over. We suggest that stem cell-driven renewal of this tegumental lineage represents an important strategy for parasite survival in the context of the host vasculature.

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Upsetting the Tree of Life

Tree of Life A nice thought piece by Ford Doolittle in PLoS Genetics. We run our first year students though this each year, so it is nice to think that some of them might find and be influenced by this article next year.

 

What Is the Tree of Life? (2016) PLoS Genet 12(4): e1005912. doi: 10.1371/journal.pgen.1005912
A universal Tree of Life has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a Tree of Life, especially as applied to prokaryotes, problematic. Lateral gene transfer is much more frequent than most biologists would have imagined up until about 20 years ago, so phylogenetic trees based on sequences of different prokaryotic genes are often different. How to tease out from such conflicting data something that might correspond to a single, universal Tree of Life becomes problematic. Moreover, since many important evolutionary transitions involve lineage fusions at one level or another, the aptness of a tree (a pattern of successive bifurcations) as a summary of life’s history is uncertain.

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RNA Bacteriophage Diversity

Bactriophage STIV2 Viruses that infect bacteria are among the most abundant life forms on Earth. Oceans and soils, and potentially even our bodies, would be overrun with bacteria were it not for bacteriophages. A new study suggests that bacteriophages with RNA genomes play a much larger role in shaping the bacterial makeup of worldwide habitats than previously recognized.

While there are numerous studies describing the role of bacteriophages with DNA genomes in ecological processes, the role of bacteriophages with RNA genomes (RNA bacteriophages) is poorly understood. This gap in knowledge is in part because of the limited diversity of known RNA bacteriophages. This research begins to address this question by identifying 122 novel RNA bacteriophage partial genome sequences present in metagenomic datasets that are highly divergent from each other and previously described RNA bacteriophages. Additionally, many of these sequences contained novel properties, including novel genes, segmentation, and host range, expanding the frontiers of RNA bacteriophage genomics, evolution, and tropism. These novel RNA bacteriophage sequences were globally distributed from numerous ecological niches, including animal-associated and environmental habitats. These findings will facilitate our understanding of the role of the RNA bacteriophage in microbial communities. There are likely many more unrecognized RNA bacteriophages that remain to be discovered.

 

Hyperexpansion of RNA Bacteriophage Diversity. (2016) PLoS Biol 14(3): e1002409. doi: 10.1371/journal.pbio.1002409
Bacteriophage modulation of microbial populations impacts critical processes in ocean, soil, and animal ecosystems. However, the role of bacteriophages with RNA genomes (RNA bacteriophages) in these processes is poorly understood, in part because of the lim- ited number of known RNA bacteriophage species. Here, we identify partial genome sequences of 122 RNA bacteriophage phylotypes that are highly divergent from each other and from previously described RNA bacteriophages. These novel RNA bacteriophage sequences were present in samples collected from a range of ecological niches worldwide, including invertebrates and extreme microbial sediment, demonstrating that they are more widely distributed than previously recognized. Genomic analyses of these novel bacterio- phages yielded multiple novel genome organizations. Furthermore, one RNA bacterio- phage was detected in the transcriptome of a pure culture of Streptomyces avermitilis, suggesting for the first time that the known tropism of RNA bacteriophages may include gram-positive bacteria. Finally, reverse transcription PCR (RT-PCR)-based screening for two specific RNA bacteriophages in stool samples from a longitudinal cohort of macaques suggested that they are generally acutely present rather than persistent.

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CRISPR-like ‘immune’ system discovered in giant virus

The MIMIVIRE defence system Giant mimiviruses fend off invaders using defences similar to the CRISPR system deployed by bacteria and other microorganisms.

Like prokaryotes, mimiviruses are plagued by viruses known as virophages. This appears to have led to the evolution of a defence system much like CRISPR in bacteria. This discovery further blurs the line between viruses and prokaryotes.

MIMIVIRE is a defence system in mimivirus that confers resistance to virophage. Nature 29 February 2016 doi: 10.1038/nature17146
Since their discovery, giant viruses have revealed several unique features that challenge the conventional definition of a virus, such as their large and complex genomes, their infection by virophages and their presence of transferable short element transpovirons. Here we investigate the sensitivity of mimivirus to virophage infection in a collection of 59 viral strains and demonstrate lineage specificity in the resistance of mimivirus to Zamilon, a unique virophage that can infect lineages B and C of mimivirus but not lineage A. We hypothesized that mimiviruses harbour a defence mechanism resembling the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system that is widely present in bacteria and archaea. We performed de novo sequencing of 45 new mimivirus strains and searched for sequences specific to Zamilon in a total of 60 mimivirus genomes. We found that lineage A strains are resistant to Zamilon and contain the insertion of a repeated Zamilon sequence within an operon, here named the ‘mimivirus virophage resistance element’ (MIMIVIRE). Further analyses of the surrounding sequences showed that this locus is reminiscent of a defence mechanism related to the CRISPR–Cas system. Silencing the repeated sequence and the MIMIVIRE genes restores mimivirus susceptibility to Zamilon. The MIMIVIRE proteins possess the typical functions (nuclease and helicase) involved in the degradation of foreign nucleic acids. The viral defence system, MIMIVIRE, represents a nucleic-acid-based immunity against virophage infection.

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Plant virus RNA silencing suppressor proteins

Lettuce necrotic yellows virus The RNA silencing pathway in plants acts in part as an antiviral defense mechanism. Plant viruses have evolved to encode suppressors of RNA silencing. Plant viral RNA silencing suppressor proteins (RSS) show little sequence conservation, but act on similar key steps in the RNA silencing pathway. Viral RSS are typically multifunctional proteins that are involved in other distinct roles such as encapsidation, cell-to-cell movement, vector transmission, replication and transcription initiation.

The majority of known plant viral RSS function by sequestering primary or secondary small interfering RNAs (siRNAs) and preventing their incorporation into the RNA induced silencing complex (RISC). However, recent insights indicate that viral RSS may compromise multiple rather than single components of the RNA silencing pathway. This study shows that the lettuce necrotic yellows virus (LNYV) P protein inhibits the activity of multiple proteins of the RNA silencing pathway, in particular, those involved in RISC and double-stranded RNA amplification.

Cytorhabdovirus P protein suppresses RISC-mediated cleavage and RNA silencing amplification in planta. (2016) Virology 22(490): 27-40. doi: 10.1016/j.virol.2016.01.003
Plant viruses have evolved to undermine the RNA silencing pathway by expressing suppressor protein(s) that interfere with one or more key components of this antiviral defense. Here we show that the recently identified RNA silencing suppressor (RSS) of lettuce necrotic yellows virus (LNYV), phosphoprotein P, binds to RNA silencing machinery proteins AGO1, AGO2, AGO4, RDR6 and SGS3 in protein-protein interaction assays when transiently expressed. In planta, we demonstrate that LNYV P inhibits miRNA-guided AGO1 cleavage and translational repression, and RDR6/SGS3-dependent amplification of silencing. Analysis of LNYV P deletion mutants identified a C-terminal protein domain essential for both local RNA silencing suppression and interaction with AGO1, AGO2, AGO4, RDR6 and SGS3. In contrast to other viral RSS known to disrupt AGO activity, LNYV P sequence does not contain any recognizable GW/WG or F-box motifs. This suggests that LNYV P may represent a new class of AGO binding proteins.

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Cyanobacteria evolved the first eyes

Micro-optic effects in cyanobacteriaCyanobacteria in the oceans are among the world’s most important oxygen producers and carbon dioxide consumers. Synechocystis is a spherical single-celled cyanobacterium that measures about three thousandths of a millimetre across. Because Synechocystis needs sunlight to produce energy, it is important for it to find places where the light is neither too weak nor too strong. Unlike some bacteria, Synechocystis can’t swim, but it can crawl across surfaces. It uses this ability to move to places where the light conditions are better.

It was already known that Synechocystis cells move towards a light source that is shone at them from one side, which implies that the cyanobacteria can “see” where the light is. But how can such a tiny cell accurately detect where light is coming from?

A paper in eLife tracked how Synechocystis moved in response to different light conditions, and found that the secret of “vision” in these cyanobacteria is that the cells act as tiny spherical lenses. When a light is shone at the cell, an image of the light source is focused at the opposite edge of the cell. Light-detecting molecules called photoreceptors respond to the focused image of the light source, and this provides the information needed to steer the cell towards the light. Although the details are different, and although a Synechocystis cell is in terms of volume about 500 billion times smaller than a human eyeball, vision in Synechocystis actually works by principles similar to vision in humans. More also remains to be learnt about how the cyanobacteria process visual information.

 

Cyanobacteria use micro-optics to sense light direction. (2016) eLife 5: e12620
Bacterial phototaxis was first recognized over a century ago, but the method by which such small cells can sense the direction of illumination has remained puzzling. The unicellular cyanobacterium Synechocystis sp. PCC 6803 moves with Type IV pili and measures light intensity and color with a range of photoreceptors. Here, we show that individual Synechocystis cells do not respond to a spatiotemporal gradient in light intensity, but rather they directly and accurately sense the position of a light source. We show that directional light sensing is possible because Synechocystis cells act as spherical microlenses, allowing the cell to see a light source and move towards it. A high-resolution image of the light source is focused on the edge of the cell opposite to the source, triggering movement away from the focused spot. Spherical cyanobacteria are probably the world’s smallest and oldest example of a camera eye.

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Adenovirus interferes with the host DNA damage response

Adenoviruses Adenoviruses (Ad) are everywhere, and while they pose limited threat in individuals with healthy immune systems, they cause significant disease burden in immunocompromised patients. A new study describes a mechanism by which the virus interferes with the host’s ability to detect and eliminate virus intruders.

The cellular DNA damage response (DDR) network interprets the presence of replicating viral DNA genomes as DNA damage and strives to repair it, leading to inhibition of virus replication. Many DNA viruses, including adenovirus, evolved mechanisms to inhibit the DDR, thus increasing the efficiency of virus replication. In this study we identify a novel mechanism used by adenovirus to inhibit the DDR. The viral E4orf4 protein, together with its cellular partner PP2A phosphatase, inhibits damage signaling by reducing phosphorylation of proteins belonging to different DDR branches. Thus inhibition of the DDR by E4orf4 contributes both to virus replication efficiency and to E4orf4-induced cancer cell killing.

E4orf4 employs a novel mechanism to inhibit the DDR, which improves Ad replication and may contribute to induction of cancer-specific cell death by the virus protein. Investigation of this novel mechanism may provide a better understanding of the DDR that is targeted by E4orf4 and required for successful application of a combinatorial treatment of cancer. Understanding the E4orf4 role in inhibition of the DDR may contribute to the development of new anti-viral and anti-cancer treatments.

 

The Adenovirus E4orf4 Protein Provides a Novel Mechanism for Inhibition of the DNA Damage Response. (2016) PLoS Pathog 12(2): e1005420. doi:10.1371/journal.ppat.1005420
The DNA damage response (DDR) is a conglomerate of pathways designed to detect DNA damage and signal its presence to cell cycle checkpoints and to the repair machinery, allowing the cell to pause and mend the damage, or if the damage is too severe, to trigger apoptosis or senescence. Various DDR branches are regulated by kinases of the phospha- tidylinositol 3-kinase-like protein kinase family, including ataxia-telangiectasia mutated (ATM) and ATM- and Rad3-related (ATR). Replication intermediates and linear double- stranded genomes of DNA viruses are perceived by the cell as DNA damage and activate the DDR. If allowed to operate, the DDR will stimulate ligation of viral genomes and will inhibit virus replication. To prevent this outcome, many DNA viruses evolved ways to limit the DDR. As part of its attack on the DDR, adenovirus utilizes various viral proteins to cause degradation of DDR proteins and to sequester the MRN damage sensor outside virus repli- cation centers. Here we show that adenovirus evolved yet another novel mechanism to inhibit the DDR. The E4orf4 protein, together with its cellular partner PP2A, reduces phos- phorylation of ATM and ATR substrates in virus-infected cells and in cells treated with DNA damaging drugs, and causes accumulation of damaged DNA in the drug-treated cells. ATM and ATR are not mutually required for inhibition of their signaling pathways by E4orf4. ATM and ATR deficiency as well as E4orf4 expression enhance infection efficiency. Furthermore, E4orf4, previously reported to induce cancer-specific cell death when expressed alone, sensitizes cells to killing by sub-lethal concentrations of DNA damaging drugs, likely because it inhibits DNA damage repair. These findings provide one explanation for the can- cer-specificity of E4orf4-induced cell death as many cancers have DDR deficiencies leading to increased reliance on the remaining intact DDR pathways and to enhanced susceptibility to DDR inhibitors such as E4orf4. Thus DDR inhibition by E4orf4 contributes both to the effi- ciency of adenovirus replication and to the ability of E4orf4 to kill cancer cells.

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