MicrobiologyBytes

First it was foot and mouth virus.
Then it was bluetongue virus.
Now it is Schmallenberg virus.
So here’s 10 things you didn’t know about Schmallenberg virus:

1. Schmallenberg virus was first isolated in Schmallenberg, Germany, in November 2011.
2. Schmallenberg virus is a Bunyavirus, one of a large group of of negative-stranded RNA viruses.
3. Why should I care? In cows, Schmallenberg virus causes fever and a drastic reduction in milk production. In sheep it causes congenital malformations and stillborn lambs (also stillborn calves in cows).
4. Schmallenberg virus was first identifed in the UK on 23rd January 2012.
5. Like Bluetongue, Schmallenberg virus is transmitted by midges (Culicoides spp.), which means we will be unlikely to be able to eradicate it – vaccination of anaimals is the only likely effective response.
6. Where did Schmallenberg virus come from? The virus genome is most closely related to sequences of a different Orthobunyavirus called Shamonda virus which belongs to the so-called Simbu serogroup known to infect ruminants and be transmitted by midges. In other words, it has form. But whether it is newly evolved (unlikely) or just newly discovered we don’t yet know.
7. How did Schmallenberg virus reach the UK? We don’t know. It could have been due to animal movements, but since it was first identifed in eastern England, it’s possible that it arrived in midges travelling under their own steam.
8. Is Schmallenberg virus going to spread to other parts of the UK and other countries? Yes, you can bet on that (just like bluetongue did).
9. Can I catch Schmallenberg virus? Honest answer: We don’t know. Possibly, but there have been no reports of human illness from areas where the virus is known to exist, so I wouldn’t worry too much.
10. Where can I find the latest news about Schmallenberg virus? Right here.
11. OK, one last time, why should I care? Because Schmallenberg virus is going to cost European and probably worldwide ecomonies millions of pounds. And that will affect you.

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I recently wrote about the top 10 plant viruses in molecular plant pathology. Well Ed didn’t like that list, so he’s published his own:

1. Tobacco mosaic virus (TMV)
2. Tomato spotted wilt virus (TSWV)
3. Tomato yellow leaf curl virus (TYLCV)
4. Cucumber mosaic virus (CMV)
5. Potato virus Y (PVY)
6. Cauliflower mosaic virus (CaMV)
7. African cassava mosaic virus (ACMV)
8. Plum pox virus (PPV)
9. Brome mosaic virus (BMV)
10. Potato virus X (PVX)

“I see only ONE virus in the major list – African cassava mosaic begomovirus (ACMV) – that infects and causes severe losses in one of the four major food crops grown on this planet: all the rest, excepting viruses infecting the also-ran potato, are pathogens of fruits, vegetables or horticulturally-important plants. Or hardly pathogenic at all, as in the case of BMV – and before anyone argues, I probably have the best collection of African (and other) isolates of the virus in the world, and a lot of experience of it in the field.”

I have a feeling this could go on for some time :-)

Many scientists, if not all, feel that their particular plant virus should appear in any list of the most important plant viruses. However, to our knowledge, no such list exists. The aim of this review was to survey all plant virologists with an association with Molecular Plant Pathology and ask them to nominate which plant viruses they would place in a ‘Top 10′ based on scientific/economic importance. The survey generated more than 250 votes from the international community, and allowed the generation of a Top 10 plant virus list including, in rank order:

• Tobacco mosaic virus
• Tomato spotted wilt virus
• Tomato yellow leaf curl virus
• Cucumber mosaic virus
• Potato virus Y
• Cauliflower mosaic virus
• African cassava mosaic virus
• Plum pox virus
• Brome mosaic virus
• Potato virus X

This review article presents a short review on each virus of the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant virology community, as well as laying down a benchmark, as it will be interesting to see in future years how perceptions change and which viruses enter and leave the Top 10.

Top 10 plant viruses in molecular plant pathology. (2011) Mol Plant Pathol. 12(9): 938-954. doi: 10.1111/j.1364-3703.2011.00752.x

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There are numerous threats facing honey bee populations and the recent losses of honey bee colonies in the United States, Canada, and Europe is alarming. In the U.S., annual honey bee colony losses increased from 17–20% to 32% during the winter of 2006/07 with some operations losing 90% of their hives. Average annual losses have remained high, averaging 32% from 2007–2010. One factor contributing to increased losses is Colony Collapse Disorder (CCD), an unexplained loss of honey bee colonies fitting a defined set of criteria. While factors such as pesticide exposure, transportation stress, genetic diversity, and nutrition affect colony health, the most significant CCD-associated variable characterized to date is increased pathogen incidence. Although greater pathogen incidence correlates with CCD, the cause is unknown in part due to insufficient knowledge of the pathogenic and commensal organisms associated with honey bees.

To gain a more complete understanding of the spectrum of infectious agents and potential threats found in commercially managed migratory honey bee colonies, researchers conducted a 10-month investigation. Analysis incorporated a suite of molecular tools (custom microarray, polymerase chain reaction (PCR), quantitative PCR (qPCR) and deep sequencing) enabling rapid detection of the presence (or absence) of all previously identified honey bee pathogens as well as facilitating the detection of novel pathogens. This study provides a comprehensive temporal characterization of honey bee pathogens and offers a baseline for understanding current and emerging threats to this critical component of U.S. agriculture.

Discovery and characterization of four new viruses will facilitate future monitoring of bee colones. Temporal characterization of these and other microbes offers a more complete view of the possible microbe-microbe and microbe-environment interactions. Further studies examining any subtle or combinatorial effects of these novel microbes are required to understand their role in colony health.

Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia. (2011) PLoS ONE 6(6): e20656. doi:10.1371/journal.pone.0020656
Honey bees (Apis mellifera) play a critical role in global food production as pollinators of numerous crops. Recently, honey bee populations in the United States, Canada, and Europe have suffered an unexplained increase in annual losses due to a phenomenon known as Colony Collapse Disorder (CCD). Epidemiological analysis of CCD is confounded by a relative dearth of bee pathogen field studies. To identify what constitutes an abnormal pathophysiological condition in a honey bee colony, it is critical to have characterized the spectrum of exogenous infectious agents in healthy hives over time. We conducted a prospective study of a large scale migratory bee keeping operation using high-frequency sampling paired with comprehensive molecular detection methods, including a custom microarray, qPCR, and ultra deep sequencing. We established seasonal incidence and abundance of known viruses, Nosema sp., Crithidia mellificae, and bacteria. Ultra deep sequence analysis further identified four novel RNA viruses, two of which were the most abundant observed components of the honey bee microbiome (~10^11 viruses per honey bee). Our results demonstrate episodic viral incidence and distinct pathogen patterns between summer and winter time-points. Peak infection of common honey bee viruses and Nosema occurred in the summer, whereas levels of the trypanosomatid Crithidia mellificae and Lake Sinai virus 2, a novel virus, peaked in January.

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Culicoides biting midges are widely distributed throughout the world and are vectors of internationally important livestock viruses, including bluetongue virus (BTV), African horse sickness virus (AHSV), Akabane virus and Epizootic haemorrhagic disease virus (EHDV). Bluetongue disease (BT) has gained considerable notoriety in recent years because of an unprecedented globalisation and climate change-mediated expansion of its range in Europe, resulting in BTV reaching areas with no historical record of the disease. The economic impact of outbreaks of BTV in these areas has been considerable as a result of both indirect costs (e.g. the restrictions placed on movement of infected ruminants) and direct losses from disease in both sheep and cattle. In addition, whilst vaccination campaigns across northern Europe eventually controlled outbreaks in this region,  it took approximately eighteen months from the initial incursion in 2006 to the deployment of vaccine in the field. During this lag period, attempts to control the spread of BTV were limited to the restriction of animal movement and the application of methods to control Culicoides midges (primarily through the use of pour-on pyrethroid insecticides to vulnerable stocks).

BTV is an arbovirus and therefore depends almost entirely on the occurrence of farm-associated populations of competent Culicoides biting midges for transmission to its ruminant hosts. As a period of extrinsic replication is required within these vectors, control measures directed at adults have the potential to reduce the spread of midge-transmitted diseases through shortening or interrupting their lifespan. Indeed, epidemiological transmission models of vector-borne diseases show that the adult lifespan is the single most important factor affecting risk of transmission. At present, the majority of approaches to control populations of biting midges are based upon the application of insecticides (primarily synthetic pyrethroids) which in northern Europe are most commonly applied to livestock, although systematic testing of compounds to date has demonstrated equivocal results. Wide scale larvicidal or adulticidal use of these compounds against Culicoides has not been considered sustainable because of the paucity of knowledge surrounding larval habitats and adult resting places, combined with increasing restrictions within the EU on untargeted use of pyrethroid insecticides. An alternative insecticide, Ivermectin, is effective in killing Culicoides species when applied intradermally or subcutaneously and also toxic to midge larvae when excreted in faeces (a potential breeding site) but has also been shown to be harmful to beneficial insects such as dung beetles. Farmers are therefore caught between the need to control populations of biting midges and the diminishing number of chemical insecticides as they are withdrawn because of their perceived risk to humans and the environment.

Entomopathogenic Fungus as a Biological Control for an Important Vector of Livestock Disease: The Culicoides Biting Midge. 2011 PLoS ONE 6(1): e16108. doi:10.1371/journal.pone.0016108
The recent outbreak of bluetongue virus in northern Europe has led to an urgent need to identify control measures for the Culicoides (Diptera: Ceratopogonidae) biting midges that transmit it. Following successful use of the entomopathogenic fungus Metarhizium anisopliae against larval stages of biting midge Culicoides nubeculosus Meigen, we investigated the efficacy of this strain and other fungi (Beauveria bassiana, Isaria fumosorosea and Lecanicillium longisporum) as biocontrol agents against adult C. nubeculosus in laboratory and greenhouse studies.
Exposure of midges to ‘dry’ conidia of all fungal isolates caused significant reductions in survival compared to untreated controls. Metarhizium anisopliae strain V275 was the most virulent, causing a significantly decrease in midge survival compared to all other fungal strains tested. The LT50 value for strain V275 was 1.42 days compared to 2.21–3.22 days for the other isolates. The virulence of this strain was then further evaluated by exposing C. nubeculosus to varying doses (108–1011 conidia m−2) using different substrates (horse manure, damp peat, leaf litter) as a resting site. All exposed adults were found to be infected with the strain V275 four days after exposure. A further study exposed C. nubeculosus adults to ‘dry’ conidia and ‘wet’ conidia (conidia suspended in 0.03% aq. Tween 80) of strain V275 applied to damp peat and leaf litter in cages within a greenhouse. ‘Dry’ conidia were more effective than ‘wet’ conidia, causing 100% mortality after 5 days.
This is the first study to demonstrate that entomopathogenic fungi are potential biocontrol agents against adult Culicoides, through the application of ‘dry’ conidia on surfaces (e.g., manure, leaf litter, livestock) where the midges tend to rest. Subsequent conidial transmission between males and females may cause an increased level of fungi-induced mortality in midges thus reducing the incidence of disease.

I’m trying to persuade a student to do my final year project next year on badger culling and bovine tuberculosis:

Bovine tuberculosis (bTB) remains an important public health concern worldwide as a result of deficiencies in preventing and/or controlling measures targeting the spread of its causative agent Mycobacterium bovis. While the risk posed by M. bovis to human health is low in most developed countries, the main causes of concern related to M. bovis in industrialized countries are epizootics in domesticated and wild mammal populations. Infection with M. bovis remains a significant livestock zoonosis in the European Union where some member states experience a reemergence of the disease despite significant historical efforts to implement eradication plans. In Great Britain, the disease was eliminated from most cattle herds by 1960, with the exception of infection hotspots in southwest England, after the implementation of a herd testing and slaughter policy. However, efforts to completely eradicate bTB in Great Britain have been hampered by the maintenance of M. bovis in wildlife host populations, acting as reservoirs of infection, in particular badgers (Meles meles). Since 1979, incidence in British cattle has increased and the infection has become more geographically widespread. Over 7 million cattle were tested for bovine bTB in 2009 and one in ten herds experienced bTB-related movement restrictions during the year as a result of at least one member of the herd failing the tuberculin skin test or showing lesions consistent with bTB during the slaughterhouse inspection – an event known as a “herd breakdown”.

Local Cattle and Badger Populations Affect the Risk of Confirmed Tuberculosis in British Cattle Herds. 2011 PLoS ONE 6(3): e18058. doi:10.1371/journal.pone.0018058
Background: The control of bovine tuberculosis (bTB) remains a priority on the public health agenda in Great Britain, after launching in 1998 the Randomised Badger Culling Trial (RBCT) to evaluate the effectiveness of badger (Meles meles) culling as a control strategy. Our study complements previous analyses of the RBCT data (focusing on treatment effects) by presenting analyses of herd-level risks factors associated with the probability of a confirmed bTB breakdown in herds within each treatment: repeated widespread proactive culling, localized reactive culling and no culling (survey-only).
Methodology/Principal Findings: New cases of bTB breakdowns were monitored inside the RBCT areas from the end of the first proactive badger cull to one year after the last proactive cull. The risk of a herd bTB breakdown was modeled using logistic regression and proportional hazard models adjusting for local farm-level risk factors. Inside survey-only and reactive areas, increased numbers of active badger setts and cattle herds within 1500 m of a farm were associated with an increased bTB risk. Inside proactive areas, the number of M. bovis positive badgers initially culled within 1500 m of a farm was the strongest predictor of the risk of a confirmed bTB breakdown.
Conclusions/Significance: The use of herd-based models provide insights into how local cattle and badger populations affect the bTB breakdown risks of individual cattle herds in the absence of and in the presence of badger culling. These measures of local bTB risks could be integrated into a risk-based herd testing programme to improve the targeting of interventions aimed at reducing the risks of bTB transmission.

Related:

• Public health and bovine tuberculosis
• Culling badgers a low priority for curbing cattle tuberculosis
• Irish badger cull ‘futile’ in controlling bovine tuberculosis

Viroids are the smallest known infectious agents and induce disease in a wide variety of plant hosts, including many crop species. Ranging in size from ca. 250–400 nucleotides (nt) replication of their single-stranded, circular, non-coding RNA genomes is entirely dependent on transcriptional and processing machinery supplied by the host. Their small size and unique molecular structure makes these molecules an attractive system with which to analyze many different aspects of host–pathogen interaction.

Although replication occurs in different subcellular compartments, members of both families of viroids induce RNA silencing and the accumulation of viroid-specific small RNAs following infection. Post-transcriptional gene silencing (RNA silencing) provides a multi-layer defense system which protects plants from invasion by exogenous RNA replicons such as viruses and viroids. Silencing is triggered by conversion of double-stranded or hairpin RNAs to small RNAs whose sizes ranging between 18 and 26 nucleotides. Infected plants contain high levels of viroid-specific small RNAs, but the circular genomic RNAs themselves appear relatively resistant to RNA silencing – raising the possibility that viroid replication may also be resistant. The mechanism underlying this resistance/tolerance is not yet understood, but certain transgenic tomato lines expressing high levels of hairpin RNA-derived small viroid RNAs are resistant to infection. This paper looks at the accumulation pattern and size distribution of viroid-specific small RNAs in infected plants and identifies several potential targets for RNA silencing mediated by small RNAs.

Accumulation of Potato spindle tuber viroid-specific small RNAs is accompanied by specific changes in gene expression in two tomato cultivars. Virology. 24 Feb 2011
To better understand the biogenesis of viroid-specific small RNAs and their possible role in disease induction, we have examined the accumulation of these small RNAs in potato spindle tuber viroid (PSTVd)-infected tomato plants. Large-scale sequence analysis of viroid-specific small RNAs revealed active production from the upper portion of the pathogenicity and central domains, two regions previously thought to be underrepresented. Profiles of small RNA populations derived from PSTVd antigenomic RNA were more variable, with differences between infected Rutgers (severe symptoms) and Moneymaker (mild symptoms) plants pointing to possible cultivar-specific differences in small RNA synthesis and/or stability. Using microarray analysis, we monitored the effects of PSTVd infection on the expression levels of >100 tomato genes containing potential binding sites for PSTVd small RNAs. Of 18 such genes down-regulated early in infection, two genes involved in gibberellin or jasmonic acid biosynthesis contain binding sites for PSTVd small RNAs in their respective ORFs.

Related:

• The Biology of Viroid-Host Interactions
• Resistance to Plant Viruses

The BSE epidemic cost us billions, and devastated the British farming industry. Now, that plague is at an end. Overall, as many as three million animals were infected; in the peak year, 1992, the UK saw 37,280 diagnoses. Yet there are good reasons why any celebrations have been put on hold. All told, around half a million infected animals entered the food chain. Although it remains unclear how many people ate the most infectious parts, it is clear that the majority of the British population was exposed. So far, the human equivalent of BSE, variant Creutzfeldt-Jakob disease (vCJD), has claimed 170 lives, mainly through consumption of BSE-infected beef. And because of the extraordinary incubation time of the disease, it is possible that many more cases may be waiting in the wings.

Read more: The end of BSE

Bacteriophages represent one of the most abundant biological entities in nature and have long been recognized for their potential use as therapeutic agents. In recent years overprescription of antibiotics and the concomitant development of antibiotic-resistant ‘super-bugs’ have highlighted the need for alternative strategies to combat infectious diseases. Consequently, a lot of phage research in the past two decades was aimed at assessing whether phage can be used to eliminate undesirable bacteria. Traceability is a requirement in modern food production, incorporating every step in the production process, commonly known as the ‘farm to fork’ concept (European Commission White paper on Food Safety, January 2000). Phages are omnipresent and are accidentally, yet regularly, consumed through ingestion of water and food. For this reason they are presumed to be safe as undesirable effects have not been reported. This, together with their specificity, makes them excellent tools for food safety purposes.

The ‘farm to fork’ concept identifies quality assurance steps at which bacterial contamination may occur, and which also represent critical points where phage treatments may be applied. The most frequently encountered food pathogens belong to one of the four dominant genera, Salmonella, enterotoxigenic Escherichia coli, Campylobacter and Listeria, along with less common infections by Clostridium spp., Staphylococcus aureus, Streptococcus suis and Cronobacter sakazakii. Phages targeting strains of each of these species have been identified and this review discusses the pros and cons of the use of phages as biocontrol, biosanitation and detection agents.

Bacteriophages as biocontrol agents of food pathogens. Curr Opin Biotechnol. Nov 4 2010
Bacteriophages have long been recognized for their potential as biotherapeutic agents. The recent approval for the use of phages of Listeria monocytogenes for food safety purposes has increased the impetus of phage research to uncover phage-mediated applications with activity against other food pathogens. Areas of emerging and growing significance, such as predictive modelling and genomics, have shown their potential and impact on the development of new technologies to combat food pathogens. This review will highlight recent advances in the research of phages that target food pathogens and that promote their use in biosanitation, while it will also discuss its limitations.

Related:

• Bugs Against Biofilms
• Bacteriophages for plant disease control
• 10 things you should know about E. coli O157