A new drug against MERS?

MERS virus Before the emergence of the highly pathogenic severe acute respiratory syndrome-associated coronavirus (SARS-CoV) in 2003 only two circulating human coronaviruses (HCoVs), HCoV- 229E and HCoV-OC43 causing relatively mild common cold-like respiratory tract infections, were known, and coronaviruses have not been regarded as significant threat for human health. Now, more than ten years later, the emergence of another highly pathogenic coronavirus of zoonotic origin, the Middle East respiratory syndrome coronavirus (MERS-CoV) points to the need for effective drugs against coronaviruses. Viruses such as coronaviruses that replicate in the host cell cytoplasm have evolved to employ host cell-derived membranes to compartmentalize genome replication and transcription. Specifically for positive-stranded RNA viruses, accumulating knowledge concerning the involvement, rearrangement and requirement of cellular membranes for RNA synthesis specify the establishment of the viral replicase complex at host cell-derived membranes as an evolution- ary conserved and essential step in the early phase of the viral life cycle.

A new paper in PLoS Pathogens describe a small molecule inhibitor of coronavirus replication that specifically targets this membrane-bound RNA replication step and has broad antiviral activity against number of diverse coronaviruses including highly pathogenic SARS-CoV and MERS-CoV. Since resistance mutations appear in an integral membrane-spanning component of the coronavirus replicase complex, and since all positive stranded RNA viruses have very similar membrane-spanning or membrane-associated replicase components implicated in anchoring the viral replication complex to host cell-derived membranes, the data suggests that the membrane-bound replication step of the viral life cycle is a novel, vulnerable, and druggable target for antiviral intervention of a wide range of RNA virus infections.

Of course clinical trials are needed before such drugs could be used, so we’re still years away from this approach being put into practce. Just in time for the next emergent coronavirus maybe?


Targeting Membrane-Bound Viral RNA Synthesis Reveals Potent Inhibition of Diverse Coronaviruses Including the Middle East Respiratory Syndrome Virus. (2014) PLoS Pathog 10(5): e1004166. doi:10.1371/journal.ppat.1004166
Coronaviruses raise serious concerns as emerging zoonotic viruses without specific antiviral drugs available. Here we screened a collection of 16671 diverse compounds for anti-human coronavirus 229E activity and identified an inhibitor, designated K22, that specifically targets membrane-bound coronaviral RNA synthesis. K22 exerts most potent antiviral activity after virus entry during an early step of the viral life cycle. Specifically, the formation of double membrane vesicles (DMVs), a hallmark of coronavirus replication, was greatly impaired upon K22 treatment accompanied by near-complete inhibition of viral RNA synthesis. K22-resistant viruses contained substitutions in non-structural protein 6 (nsp6), a membrane-spanning integral component of the viral replication complex implicated in DMV formation, corroborating that K22 targets membrane bound viral RNA synthesis. Besides K22 resistance, the nsp6 mutants induced a reduced number of DMVs, displayed decreased specific infectivity, while RNA synthesis was not affected. Importantly, K22 inhibits a broad range of coronaviruses, including Middle East respiratory syndrome coronavirus (MERS–CoV), and efficient inhibition was achieved in primary human epithelia cultures representing the entry port of human coronavirus infection. Collectively, this study proposes an evolutionary conserved step in the life cycle of positive-stranded RNA viruses, the recruitment of cellular membranes for viral replication, as vulnerable and, most importantly, druggable target for antiviral intervention. We expect this mode of action to serve as a paradigm for the development of potent antiviral drugs to combat many animal and human virus infections.


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Antibiotics – let's clean up our act

East Penobscot Bay, Maine by Jason Mrachina

Beautiful Penobscot Bay

Last week I wrote about a new type of antibiotic which targets bacteria in biiofilms. Ron Huber (Friends of Penobscot Bay) left an interesting comment:

“Of concern to us as … conservationists is whether these broad spectrum peptide antibiotics are digested by standard sewage treatment plant technology or pass essentially unscathed through the patient and the wastewater treatment facility and into the receiving waters. We want and absolutely need vigorous marine biofilms, an at a variety of scales and species mixes, if we are to have mussels, lobsters, clams, oysters and other organisms at all… Sewage plants are adaptable; can something be added that would bind with the antibiotic or otherwise render it harmless before discharge We would really like to know!” (full comment)

There has been much discussion about the misuse of antibiotics in agriculture and the impact of such careless use on human health. There has been rather less public discuss on on the environmental impact of antibiotic resides in sewage effluent. So apart from the environment, do antibiotic residues which survive sewage pose a risk to human health?

Yes they do (Selective pressure of antibiotic pollution on bacteria of importance to public health. (2012) Environmental health perspectives, 120(8), 1100). Consequently, there is a fair amount of research being carried out in this area – it just doesn’t make it into the press. Standard sewage treatment processes reduce but don’t eliminate antibiotics in sewage and these can contribute to the evolution and persistence of resistant pathogens in the environment (The effectiveness of sewage treatment processes to remove faecal pathogens and antibiotic residues. (2012) Journal of Environmental Science and Health, Part A, 47(2), 289-297). This paper shows that more advanced treatments such as membrane bioreactor technology reduce antibiotic resides more than the conventional activated sludge process, but still do not eliminate them completely from the wastewater.

What effect do these residues have on the environment? We really don’t know, but it seems likely that legislators are more likely to respond to the costs involved in improving sewage treatment via the human health argument rather than the environmental argument. Sad, but that’s how it is. As far as the new peptide antibiotic I wrote about last week is concerned, we simply don’t know yet how it will be affected by sewage treatment processes. But should we be worried about such criteria when introducing new compounds for therapeutic use? Yes we should. Of course, it’s not just antibiotics we have to worry about.


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New Broad-Spectrum Peptide Antibiotic Targets Biofilms

Biofilm Biofilms are structured multicellular communities of microorganisms associated with surfaces. They have been widely studied, in part because they cause at least 65% of all human infections, being particularly prevalent in device-related infections, on body surfaces and in chronic infections. Biofilms represent a major health problem worldwide due to their resistance to host defence mechanisms and to conventional antimicrobials, which generally target free-swimming (planktonic) bacteria. So there is an urgent need to identify compounds that effectively clear biofilm-related infections.

A new report in PLoS Pathogens identifies a potent anti-biofilm peptide that works by blocking (p)ppGpp, an important signal in biofilm development. The peptide had at least three effects on biofilms, which might reflect the role of (p)ppGpp in cells. First when added prior to initiation of biofilms it prevented biofilm formation, second it specifically led to cell death in biofilms at concentrations that were not lethal for planktonic (free-swimming) cells, and third it promoted biofilm dispersal even in maturing (2-day old) biofilms. This anti-biofilm strategy represents a significant advance in the search for new agents that specifically target many bacterial species.


Broad-Spectrum Anti-biofilm Peptide That Targets a Cellular Stress Response. (2014) PLoS Pathog 10(5): e1004152. doi:10.1371/journal.ppat.1004152
Bacteria form multicellular communities known as biofilms that cause two thirds of all infections and demonstrate a 10 to 1000 fold increase in adaptive resistance to conventional antibiotics. Currently, there are no approved drugs that specifically target bacterial biofilms. Here we identified a potent anti-biofilm peptide 1018 that worked by blocking (p)ppGpp, an important signal in biofilm development. At concentrations that did not affect planktonic growth, peptide treatment completely prevented biofilm formation and led to the eradication of mature biofilms in representative strains of both Gram-negative and Gram-positive bacterial pathogens including Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, methicillin resistant Staphylococcus aureus, Salmonella Typhimurium and Burkholderia cenocepacia. Low levels of the peptide led to biofilm dispersal, while higher doses triggered biofilm cell death. We hypothesized that the peptide acted to inhibit a common stress response in target species, and that the stringent response, mediating (p)ppGpp synthesis through the enzymes RelA and SpoT, was targeted. Consistent with this, increasing (p)ppGpp synthesis by addition of serine hydroxamate or over-expression of relA led to reduced susceptibility to the peptide. Furthermore, relA and spoT mutations blocking production of (p)ppGpp replicated the effects of the peptide, leading to a reduction of biofilm formation in the four tested target species. Also, eliminating (p)ppGpp expression after two days of biofilm growth by removal of arabinose from a strain expressing relA behind an arabinose-inducible promoter, reciprocated the effect of peptide added at the same time, leading to loss of biofilm. NMR and chromatography studies showed that the peptide acted on cells to cause degradation of (p)ppGpp within 30 minutes, and in vitro directly interacted with ppGpp. We thus propose that 1018 targets (p)ppGpp and marks it for degradation in cells. Targeting (p)ppGpp represents a new approach against biofilm-related drug resistance.


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Oncolytic virotherapy – in pets?

Oncolytic viruses Oncolytic virotherapy – using viruses to treat cancer – is a hot topic. Earlier this week the media was reporting a new clinical trial where researchers seeming cured multiple myeloma in one patient by giving her a huge dose of measles vaccine (NHS Choices: Measles virus used to treat bone marrow cancer). But cancer is among the top fatal diseases in domestic and feral dogs and cats too. Incidence of canine or feline cancer ranges from 1% to 2% and cancer currently accounts for about half of the deaths of domestic animals older than 10 years. The most common forms of cancer in dogs and cats are skin, lymphoma, mammary, bone, connective tissue, and oral cancers. The traditional and established methods for pet cancer treatment include surgery, radiation therapy, chemotherapy, hyperthermia and photodynamic therapy. However, the available treatment options for pets with advanced-stage disease are limited and the prognosis for such animals is very poor.

The first clinical studies with vaccinia and adenovirus for canine cancer therapy are underway and data on clinical effectiveness is awaited. As for oncolytic virotherapy of human cancers, the most important challenges for the successful clinical use of OVs in veterinary practice are reduction of viral toxicity, optimization of virus delivery to tumor, and enhancement of viral spread throughout the tumor mass. So will it catch on?


Oncolytic Virotherapy of Canine and Feline Cancer. Viruses 2014, 6(5), 2122-2137; doi:10.3390/v6052122
Cancer is the leading cause of disease-related death in companion animals such as dogs and cats. Despite recent progress in the diagnosis and treatment of advanced canine and feline cancer, overall patient treatment outcome has not been substantially improved. Virotherapy using oncolytic viruses is one promising new strategy for cancer therapy. Oncolytic viruses (OVs) preferentially infect and lyse cancer cells, without causing excessive damage to surrounding healthy tissue, and initiate tumor-specific immunity. The current review describes the use of different oncolytic viruses for cancer therapy and their application to canine and feline cancer.



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Emerging Disease or Emerging Diagnosis?

Toward the end of the 20th century, deadly microbes seemed to be springing up out of nowhere: Lassa virus in 1969, Ebola virus in 1976 and HIV in the 1980s. Public health officials classified them as “emerging diseases,” meaning they are newly introduced or rising rapidly in human populations. Recent data, however, suggest these viruses may instead have been circulating widely for hundreds or thousands of years. We may not be contending with emerging disease at all, but emerging diagnosis of ancient and frequent disease. This paradigm shift has implications towards countering these viruses now before they become global threats.

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Further delay before the end of smallpox virus?

Smallpox vaccine Variola, the virus that causes smallpox, is on the agenda of the upcoming meeting of the World Health Assembly (WHA), the governing body of the World Health Organization. The decision to be made is whether the last known remaining live strains of the virus should be destroyed. An international group of scientists argue in an opinion piece published on May 1st in PLOS Pathogens that the WHA should not choose destruction, because crucial scientific questions remain unanswered and important public health goals unmet.

Smallpox was declared eradicated in 1980, the only human pathogen for which successful eradication has been achieved to date. Since then, limited research focusing on diagnostic, antiviral and vaccine development, under close direction and oversight, has continued in two high-security laboratories – one in Russia and one in the US – the only places that are known still to have live variola strains. The justification for this research is that smallpox might re-appear via intentional release. Indeed, recent advances in synthetic biology make the possibility of re-creating the live virus from scratch more plausible.

Summarizing the focus and the achievements of the research on live variola over the past several decades, the authors of the PLOS Pathogens article mention several new smallpox vaccines (the ones widely used prior to eradication would not meet today’s stricter safety standards for routine use) and two new drug candidates that, based on research so far, appear to be promising antivirals against the virus that causes smallpox. However, both of these drug candidates have not yet been licensed for use against the disease. “Despite these considerable advances, they argue that “the research agenda with live variola virus is not yet finished”.

Are We There Yet? The Smallpox Research Agenda Using Variola Virus. (2014) PLoS Pathog 10(5): e1004108. doi:10.1371/journal.ppat.1004108

Should Remaining Stockpiles of Smallpox Virus Be Destroyed?


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Science communication: a communicable disease?

At the Society’s 2014 Annual Conference, Professor Stephen Curry was awarded the Peter Wildy Prize. This is his prize lecture, in which he describes how he became involved in science communication and why it is an important discipline for researchers to be involved in.

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CRISPRs and bacterial pathogenesis

CRISPRs have taken microbiology by storm in the last few years. If you haven’t caught up yet, there’s a short introductory primer here. CRISPRs (or CRISPR-Cas systems as they are now tending to be called) protect bacteria from infection by bacteriophages and other mobile genetic elements including plasmids. Because they are barriers to horizontal gene transfer, CRISPRs reduce the speed of eviolution of pathogens. but CRISPRs can increase also virulence by modulating gene expression. A recent short review discusses the “love-hate relationship between bacterial pathogens and their CRISPR-Cas systems“.

CRISPR-Cas system

Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens. (2014) Current Opinion in Microbiology, 17, 82-90.
CRISPR-Cas systems protect prokaryotes from viruses and plasmids and function primarily as an adaptive immune system in these organisms. Recent discoveries, however, revealed unexpected roles for CRISPR loci as barriers to horizontal gene transfer and as modulators of gene expression. We review how both of these functions of CRISPR-Cas systems can affect the emergence and virulence of human bacterial pathogens.



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A global network of researchers? Not really – small worlds.

As science evolves, important scientific achievements require the collaborative effort of an increasing number of researchers. The study of patterns of scientific collaboration allows us to gain further understanding of innovation and knowledge production. Scientific collaboration networks have been the subject of growing interest in the past few years. Collaborative scientific publications have a long history. The first collaborative research paper was published in 1665 in the Philosophical Transactions of the Royal Society. To date, the most multi-authored scientific paper was published in 2010, when 3,222 researchers from 32 different countries contributed to a study of charged-particle multiplicities performed in the Large Hadron Collider at CERN.

A new study finds that the United States was the country with the largest number of international collaborations, particularly with South Africa, Uganda and Brazil. The high global clustering coefficient coupled with a short average distance between nodes suggests a “small-world phenomenon” among HIV and HPV researchers. Researchers from high-income countries seem to have a high number of research collaborations among them and to cluster together in densely connected communities, particularly those from the US. There is a large well-connected community, which encompasses 70% of researchers, and other much smaller communities, including the UK.

Small worlds

International Scientific Collaboration in HIV and HPV: A Network Analysis. (2014) PLoS ONE 9(3): e93376. doi:10.1371/journal.pone.0093376
Research endeavours require the collaborative effort of an increasing number of individuals. International scientific collaborations are particularly important for HIV and HPV co-infection studies, since the burden of disease is rising in developing countries, but most experts and research funds are found in developed countries, where the prevalence of HIV is low. The objective of our study was to investigate patterns of international scientific collaboration in HIV and HPV research using social network analysis. Through a systematic review of the literature, we obtained epidemiological data, as well as data on countries and authors involved in co-infection studies. The collaboration network was analysed in respect to the following: centrality, density, modularity, connected components, distance, clustering and spectral clustering. We observed that for many low- and middle-income countries there were no epidemiological estimates of HPV infection of the cervix among HIV-infected individuals. Most studies found only involved researchers from the same country (64%). Studies derived from international collaborations including high-income countries and either low- or middle-income countries had on average three times larger sample sizes than those including only high-income countries or low-income countries. The high global clustering coefficient (0.9) coupled with a short average distance between researchers (4.34) suggests a “small-world phenomenon.” Researchers from high-income countries seem to have higher degree centrality and tend to cluster together in densely connected communities. We found a large well-connected community, which encompasses 70% of researchers, and 49 other small isolated communities. Our findings suggest that in the field of HIV and HPV, there seems to be both room and incentives for researchers to engage in collaborations between countries of different income-level. Through international collaboration resources available to researchers in high-income countries can be efficiently used to enroll more participants in low- and middle-income countries.

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