Nanobot viruses tag and round up bacteria in food and water

A PR which continues with the we’re-all-hosts-on-a-viral-planet themed, but gives some advice about how to work with nature to achieve goals.

Viruses engineered into “nanobots” can find and separate bacteria from food or water.

These viruses, called bacteriophages or just phages, naturally latch onto bacteria to infect them (SN: 7/12/03, p. 26). By tweaking the phages’ DNA and decking them out with magnetic nanoparticles, researchers created a tool that could both corral bacteria and force them to reveal themselves. These modifications can boost the sensitivity and speed of rooting out bacteria in tainted food or water, the researchers reported March 20 at the annual meeting of the American Chemical Society.

“You’re taking the power of what evolution has done … to bind bacteria, and then we’re just helping that out a little bit,” said Sam Nugen, a food and biosystems engineer who leads the team designing these phages at Cornell University.

Competing technologies for detecting bacteria use antibodies, the product of an immune response. But these are expensive to produce and work best in a narrow temperature and pH range. In contrast, phages “exist everywhere,” making them potentially more broadly useful as bacteria hunters, Nugen said. “They’ve had to evolve to bind well in much broader conditions than antibodies.”

Phages identify and grab bacteria using proteins on their leglike tail fibers, which form a strong bond with compounds on the bacterial cell surface. To infect the cell, the phage injects its genetic material. This hijacks the cell, forcing its machinery to produce phage clones.

Nugen and collaborators programmed phages to tag E. coli bacteria. The team’s engineered phages contained extra DNA that told the bacteria to make an easily detectable enzyme. When the infection caused the bacterial cells to rupture and release the new phages, a chemical reaction involving the enzyme produced a measurable signal: light, color or an electric current. For example, the phages exposed E. coli in milk and orange juice by turning the liquids red or pink.

The researchers also loaded the phages with nanoparticles with a magnetic iron and cobalt core. Once the phages latched onto the bacteria, researchers could use a magnet to round the bacteria up even before the bacteria ruptured and announced their presence. This allowed the researchers to detect low concentrations of bacteria: less than 10 E. coli cells in half a cup of water. Conventional methods grow the bacteria into colonies to find them, which can take up to two days. But using the phages, Nugen and his colleagues skipped this step and found the cells within a few hours.

Using phages for magnetic separation would be “really nice for food and environmental samples because they tend to be really dirty,” said Michael Wiederoder, a bioengineer at the U.S. Army Natick Soldier Research, Development and Engineering Center in Massachusetts, who was not involved in the research. The salt, sugar and fats in food can slow the reactions of antibody-based tests, he said.

Also, the phages infect only bacteria that can reproduce, allowing testers to tell the difference between live cells and those killed by antibiotics, heat or chlorine. With food, “whether the bacteria are alive or dead is the difference between you getting sick and not,” Wiederoder said.

The nanobots could also prove useful for blood or other human samples. There, phages would provide a way to find resistant bacteria left alive after a course of antibiotics.

The next challenge: tinkering with the phages to tune which bacteria they go after. In nature, phages prey on specific species. But in food, it may be helpful to detect several common offenders, like E. coli, Salmonella and Listeria, or, alternatively, to have greater discrimination to find only the pathogenic E. coli and leave the rest.

We’re all hosts on a viral planet: Trillions upon trillions of viruses fall from the sky each day

When a stoned Carl Sagan used to do his TV bit and talk about billions and billions of galaxies, I turned my world inward, to the trillions and trillions of viruses.

I tell daughter Sorenne, I don’t care which you focus on, but get one of them right.

According to Jim Robbins of the New York Times, high in the Sierra Nevada mountains of Spain, an international team of researchers set out four buckets to gather a shower of viruses falling from the sky.

Scientists have surmised there is a stream of viruses circling the planet, above the planet’s weather systems but below the level of airline travel. Very little is known about this realm, and that’s why the number of deposited viruses stunned the team in Spain. Each day, they calculated, some 800 million viruses cascade onto every square meter of the planet.

Most of the globe-trotting viruses are swept into the air by sea spray, and lesser numbers arrive in dust storms.

“Unimpeded by friction with the surface of the Earth, you can travel great distances, and so intercontinental travel is quite easy” for viruses, said Curtis Suttle, a marine virologist at the University of British Columbia. “It wouldn’t be unusual to find things swept up in Africa being deposited in North America.”

The study by Dr. Suttle and his colleagues, published earlier this year in the International Society of Microbial Ecology Journal, was the first to count the number of viruses falling onto the planet. The research, though, is not designed to study influenza or other illnesses, but to get a better sense of the “virosphere,” the world of viruses on the planet.

Generally it’s assumed these viruses originate on the planet and are swept upward, but some researchers theorize that viruses actually may originate in the atmosphere. (There is a small group of researchers who believe viruses may even have come here from outer space, an idea known as panspermia.)

Whatever the case, viruses are the most abundant entities on the planet by far. While Dr. Suttle’s team found hundreds of millions of viruses in a square meter, they counted tens of millions of bacteria in the same space.

Mostly thought of as infectious agents, viruses are much more than that. It’s hard to overstate the central role that viruses play in the world: They’re essential to everything from our immune system to our gut microbiome, to the ecosystems on land and sea, to climate regulation and the evolution of all species. Viruses contain a vast diverse array of unknown genes — and spread them to other species.

Last year, three experts called for a new initiative to better understand viral ecology, especially as the planet changes. “Viruses modulate the function and evolution of all living things,” wrote Matthew B. Sullivan of Ohio State, Joshua Weitz of Georgia Tech, and Steven W. Wilhelm of the University of Tennessee. “But to what extent remains a mystery.”

We’re all hosts on a viral planet.

I didn’t understand this until fourth-year university, and it was only then I became interested in learning.

Until then, I was bored.

Researchers recently identified an ancient virus that inserted itDNA into the genomes of four-limbed animals that were human ancestors. That snippet of genetic code, called ARC, is part of the nervous system of modern humans and plays a role in human consciousness — nerve communication, memory formation and higher-order thinking. Between 40 percent and 80 percent of the human genome may be linked to ancient viral invasions.

Viruses and their prey are also big players in the world’s ecosystems. Much research now is aimed at factoring their processes into our understanding of how the planet works.

“If you could weigh all the living material in the oceans, 95 percent of it is stuff is you can’t see, and they are responsible for supplying half the oxygen on the planet,” Dr. Suttle said.

In laboratory experiments, he has filtered viruses out of seawater but left their prey, bacteria. When that happens, plankton in the water stop growing. That’s because when preying viruses infect and take out one species of microbe — they are very specific predators — they liberate nutrients in them, such as nitrogen, that feed other species of bacteria. In the same way, an elk killed by a wolf becomes food for ravens, coyotes and other species. As plankton grow, they take in carbon dioxide and create oxygen.

One study estimated that viruses in the ocean cause a trillion trillion infections every second, destroying some 20 percent of all bacterial cells in the sea daily.

Viruses help keep ecosystems in balance by changing the composition of microbial communities. As toxic algae blooms spread in the ocean, for example, they are brought to heel by a virus that attacks the algae and causes it to explode and die, ending the outbreak in as little as a day.

While some viruses and other organisms have evolved together and have achieved a kind of balance, an invasive virus can cause rapid, widespread changes and even lead to extinction.

 

Gastro outbreak hits more than 50 day care centres in Brisbane

It’s winter in Brisbane, Australia, with highs in the 90s F (30s C) a couple of weeks ago, and today where I went to the arena for a lunchtime skate with Amy in shorts and the loudest Hawaiian shirt I own (additional layers were added once in the arena), and where what they call gastro outbreaks have increased dramatically.

Seven elderly people have died from gastro at one Brisbane nursing home – vigorously denied by the operator – and more than 50 daycare centres have alerted Queensland Health of gastro outbreaks.

Emergency rooms throughout Brisbane have been overwhelmed, and not just by dumbass Canadians falling off bikes.

But what is a gastro bug?

How can they not name the bug?

Regis aged care facility in the suburb of Yeronga, just down the road from us, has been in lockdown for 26 days.

A Regis spokesperson on Tuesday night reiterated “there have been no deaths confirmed as being as a result of gastro.”

“As advised previously, Regis has experienced an episode of gastroenteritis at the Yeronga facility. It was first identified on 28 July. We are pleased to say that the episode is nearing completion.”

Darren Cartwright of the Courier-Mail reported yesterday there has been a four-fold increase in gastroenteritis outbreaks in Brisbane’s daycare centres, with almost 200 children alone affected on the southside since June.

In total more than 50 daycare centres have alerted Queensland Health of an outbreak of gastroenteritis.

A Queensland Health spokesman acknowledged the outbreaks were “significantly” higher this year than for the same eight week periods in 2016.

“The data indicates a significantly high number of outbreaks during this eight week period in 2017, however, it should be noted that half of these outbreaks involved fewer than 10 unwell children,” the spokesman said.

That will make the parents and kids feel better.

“In general, it has been a big year for viral gastroenteritis outbreaks across the region.”

Oh, it’s a virus.

Does the virus have a name?

 

We’re all hosts on a viral planet: New virus breaks the rules of infection

Michaeleen Doucleff of North Carolina Public Radio writes that human viruses are like a fine chocolate truffle: It takes only one to get the full experience.

283615-virusAt least, that’s what scientists thought a few days ago. Now a new study published Thursday is making researchers rethink how some viruses could infect animals.

A team at the U.S. Army Medical Research Institute of Infectious Diseases has found a mosquito virus that’s broken up into pieces. And the mosquito needs to catch several of the pieces to get an infection.

“It’s the most bizarre thing,” says Edward Holmes, a virologist at the University of Sydney, who wasn’t involved in the study. It’s like the virus is dismembered, he says.

“If you compare it to the human body, it’s like a person would have their legs, trunk and arms all in different places,” Holmes says. “Then all the pieces come together in some way to work as one single virus. I don’t think anything else in nature moves this way.”

Most viruses have simple architecture. They have a few genes — say about a half-dozen or so — that are packaged up into a little ball, 1/500th the width of a human hair.

“You can think of it like a teeny-weeny tennis ball with spikes,” Holmes says.

When the virus infects a cell, the ball latches onto the cell’s surface, opens up and pops its genes into the cell.

Poof! The cell is infected. That’s all it takes. One ball, sticking to one cell.

But that’s not the case for the Guaico Culex virus. It has five genes. And each one gets stuffed into a separate ball. Imagine five tennis balls, each with a different color: a red tennis ball, a blue one, a green one, a yellow one and an orange one.

Then to get infected with the virus, a mosquito needs to catch at least four different colored balls, researchers write in the journal Cell Host & Microbe. Otherwise the infection fails.

“The fifth ball seems to be optional,” says Jason Ladner, a genomicist at USAMRIID, who helped discover the virus. Getting the fifth one could control how dangerous the virus is, he says.

Ladner and his team found the virus inside a Culex mosquito found in Guaico, Trinidad — hence the name of the virus, Guaico Culex. Culex mosquitoes are common across the U.S. and spread West Nile Virus.

The study is part of a larger project aimed at figuring out what viruses, in addition to Zika and yellow fever, could be lurking inside mosquitoes and possibly waiting to spill over into people.

Indeed, each year, scientists are finding thousands of new viruses, says Vincent Racaniello, at Columbia University. “It’s hard to put a number on it. But it’s huge.”

“We finally have the tools to find them,” he says.

But that doesn’t mean we can immediately understand what they do, or even whom they infect.

“There’s so much we don’t know about viruses,” Racaniello adds. And with viruses, really anything is possible. “We should always expect the unexpected,” he says.

 

I miss my hot tub, I miss my sauna, I don’t miss the viruses

From August to September 2014 a water quality study was conducted on five popular public Danube beaches in Vojvodina, Serbia.

serbia.beach.waterTo assess the safety of Danube water for bathing, physical, chemical, bacteriological tests were performed. While many parameters for monitoring the quality of water are regulated by law, there are neither national nor international legislations addressing the presence of viruses in recreational waters. In this study, we performed analyses that surpassed national requirements, and investigated if adenovirus, enterovirus or rotavirus genetic material was present in samples of recreational water collected for quality monitoring.

Of 90 water samples obtained during the study, enterovirus material was not found in any sample, but adenovirus and rotavirus genetic materials were respectively detected in 60 and 31 samples. Statistical analyses showed a significant correlation between adenovirus DNA and total coliforms in the water. Even when water samples were adequate for recreational use, adenoviruses were detected in 75% (57/76) of such samples. Our results indicate that implementation of viral indicators in recreational water might be helpful to better assess public health safety. This might be particularly relevant in areas where urban wastewater treatment is insufficient and surface waters affected by wastewater are used for recreation.

Testing For Viral Material In Water Of Public Bathing Areas Of The Danube During Summer, Vojvodina, Serbia, 2014

Eurosurveillance, Volume 21, Issue 15, 14 April 2016

A Jovanović Galović, S Bijelović, V Milošević, I Hrnjaković Cvjetkovic, M Popović, G Kovačević , J Radovanov, N Dragić, V Petrović

http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=21441

It’s not the curves, it’s the oxygen groups: Viral attachment to produce

In an effort to understand and eventually reduce the incidence of foodborne illnesses, University of Illinois researchers studied the ability of pathogenic viruses to adhere to fresh produce surfaces.

lettuce“We chose 24 of the most common salad vegetables in the U.S. and assayed them to see if there was any relationship between the morphology and chemistry of the leaf or fruit surface and the adherence of viral particles, before and after a washing treatment,” says U of I geneticist Jack Juvik.

The researchers inoculated leafy salad greens and tomatoes with a swine virus that mimics human rotavirus, a common pathogen responsible for diarrhea, vomiting, fever, and abdominal pain. After exposing the vegetable surfaces to the virus, the researchers rinsed the vegetables twice with a standard saline solution.

“We correlated virus adherence to roughness of the surface at different scales. We also looked at the chemistry of the proteins and waxes associated with the leaf cuticle – a waxy layer that protects the plant against diseases and reduces water loss,” Juvik explains. “Before this, no one had tested the relationship between chemistry and surface texture on the adherence of virus particles.”

The researchers found a thousand-fold difference in the number of viral particles adhering to different types of leafy greens and tomatoes. Vegetables with three-dimensional crystalline wax structures on the leaf cuticle harbored significantly fewer virus particles after rinsing. This was counterintuitive, as it was expected that small virus particles could “hide” in the rough structures of these cuticles.

lettuce.nov10“I was surprised, too,” Juvik says. “But normally, viruses adhere to oxygen groups, like OH, which are associated with proteins and carbohydrates on the surface. When the wax completely covers the surface, it becomes totally hydrophobic, which renders the whole leaf surface harder for viruses to attach to. Furthermore, rinsing those leaves with water gives the viruses the OH groups they’re looking for, so they’re easier to wash away.”

Produce is exposed to viruses and other pathogens in a number of ways, including contaminated irrigation water, animal wastes, and handling by sick workers. But because salad vegetables are consumed fresh, pathogens cannot be killed by cooking or most other sterilization methods.

“Viruses are literally everywhere, causing many opportunities for infection. But the information from this study can be used down the road to select or breed for varieties that might have the capacity to reduce adherence of these particles,” Juvik explains.

The researchers have already repeated the study using the bacterium E. coli, but they plan to look at even more vegetable varieties and pathogens in future studies.

The article, “Influence of epicuticular physiochemical properties on porcine rotavirus adsorption to 24 leafy green vegetables and tomatoes” was published in PLOS One. The study was led by Lu Lu, whose co-authors included Juvik, Kang-Mo Ku, Sindy Paola Palma-Salgado, Andrew Page Storm, Hao Feng, and Thanh Nguyen, all from the University of Illinois. The project received funding from the USDA’s National Institute of Food and Agriculture.

Foodborne viruses in fresh produce

Norovirus (NoV) and hepatitis A virus (HAV) are the most important foodborne viruses. Fresh produce has been identified as an important vehicle for their transmission.

foodborne.virus.produceIn order to supply a basis to identify possible prevention and control strategies, this review intends to demonstrate the fate of foodborne viruses in the farm to fork chain of fresh produce, which include the introduction routes (contamination sources), the viral survival abilities at different stages, and the reactions of foodborne viruses towards the treatments used in food processing of fresh produce. In general, the preharvest contamination comes mainly from soli fertilizer or irrigation water, while the harvest and postharvest contaminations come mainly from food handlers, which can be both symptomatic and asymptomatic. Foodborne viruses show high stabilities in all the stages of fresh produce production and processing. Low-temperature storage and other currently used preservation techniques, as well as washing by water have shown limited added value for reducing the virus load on fresh produce. Chemical sanitizers, although with limitations, are strongly recommended to be applied in the wash water in order to minimize cross-contamination. Alternatively, radiation strategies have shown promising inactivating effects on foodborne viruses. For high-pressure processing and thermal treatment, efforts have to be made on setting up treatment parameters to induce sufficient viral inactivation within a food matrix and to protect the sensory and nutritional qualities of fresh produce to the largest extent.

Comprehensive Reviews in Food Science and Food Safety

Dan Li, Ann De Keuckelaere and Mieke Uyttendaele

UK version: Viruses in the food chain

In 1994, in response to the outcomes of a joint Advisory Committee of Microbiological Safety of Food (ACMSF) and Steering Group on the Microbiological Safety of Food (SGMSF) meeting, a Working Group was set up to investigate the science and epidemiology of Foodborne Viral Infections.

virus.foodThe Working Group assessed the risk from viruses that were believed to be the primary cause of foodborne illness. This report provides an update to this information and provides a new focus on the viruses which are currently the major route of foodborne illness. Since the publication of the 1998 report, with the exception of two minor risk assessments on hepatitis E and avian influenza, no formal review on viruses had been performed by the ACMSF. It was decided that as significant developments had been made not only in the detection of foodborne viruses, but also in the amount of information obtained from the Infectious Intestinal Disease (IID) Study in England (published in 2000), which indicated a significant disease burden from enteric viruses in the community, it was important that an Ad-Hoc Group was convened to revisit these issues and to provide an update to the 1998 risk assessment.

The FVI Group first met to begin their consideration in November 2010. Over 32 months, the Group met thirteen times to discuss all aspects of viruses in the food chain from farm to fork. As a starting point for the report, the Group reviewed the recommendations from the 1998 report and gave consideration as to whether these had been adequately addressed or were still relevant. At the same time the recommendations from the 2008 World Health Organisation (WHO) Viruses in Food: Scientific Advice to Support Risk Management Activities Matrix and CODEX Criteria, and the European Food Safety Authority (EFSA) Scientific Opinion on an update on the present knowledge on the occurrence and control of foodborne viruses were reviewed.

Using this information along with data on disease burden in the community and outbreak data (from IID and IID2) the Group agreed the scope of the report and what viruses would be its main focus. It was decided that that due to their potential impact and the paucity of data in this area, norovirus, hepatitis E and hepatitis A would be the main focus of the report, although many of the recommendations would also be applicable to other enteric viruses.

During its consideration, the Group reviewed available data on commodities contaminated at source, i.e. bivalve shellfish, pork products and fresh produce and reviewed data on risks associated with infected food handlers. Environmental contamination was reviewed with consideration given to testing methods such as polymerase chain reaction (PCR), person-to-person transmission and food handlers. The Group also considered the engagement with industry and other Government departments (OGDs) regarding environmental conditions of shellfish waters and its impact on norovirus.

A review of data on issues regarding food contact surface contamination, including survivability and persistence was considered along with options for control at all stages of the food chain e.g. thermal processing, storage etc. The thermal stability of hepatitis E was considered with data presented on the increasing occurrence of the disease particularly in older UK males and the recent case control study on the association with processed pork products.

In order to obtain sentinel data the group investigated the important issue of knowledge gathering and surveillance data regarding foodborne viruses. The current limitations of the data were discussed along with what type of data was needed to provide more useful/accurate information on foodborne virus outbreaks. This review included looking at outbreaks from an Environmental Health Officer (EHO) perspective and how they prioritise what they investigate and the data they collect.

Finally, the group reviewed the consumer perspective on risk. This included looking at how risk is presented and information distributed, as this was likely to impact on any future risk assessment.

Within the report the Group has endeavoured to prioritise the recommendations by separating these into those that will inform risk assessments and those that will impact on risk assessments. Full details are provided in the report; however, key recommendations include:

A better understanding of ‘foodborne viral disease’ (Chapter 3) is required by investigating the correlation between infective dose and genome titre. Molecular diagnostics, typing and quantification should also be used to better understand the burden of virus contamination in foodstuffs. Work is also recommended to develop the methods used to assess norovirus and hepatitis E infectivity in food samples. This would better inform surveys and could potentially be applied to routine monitoring.

Improved ‘routine surveillance and investigation of foodborne viruses’ (Chapter 5) is required with Government agencies developing a single integrated outbreak reporting scheme. A joined up approach that would also involve the annual consolidation of records would reduce the chance of underreporting outbreaks. Further to this, reliable methods for norovirus whole genome sequencing should be developed to enable virus tracking and attribution.

More research on the ‘contamination of food’ (Chapter 6) through sewage contamination is recommended. In particular work should investigate the effectiveness of sewage treatment processes in reducing norovirus concentrations, including the use of depuration on shellfish species and disinfection treatments. Similarly, research is needed to identify the most effective means of decontaminating ‘fresh produce’ post-harvest (Chapter 7).

With the emerging risk of hepatitis E in pigs, the Group recommends work is undertaken to investigate the heat inactivation of hepatitis E in ‘pork products’ (Chapter 8). Research on the effect of curing and fermentation on hepatitis E in pork products is also recommended.

The full list of conclusions and recommendation are presented at the end of each subject area and are consolidated in Chapter 12 for ease of reference.

The assessments made and conclusions reached by the Group reflect evidence oral and written drawn from the scientific community, Government departments and Agencies, EFSA and the scientific literature. The Group’s full conclusions, identified data gaps and recommendations are brought together at the end of this report. The ACMSF accepts full responsibility for the final content of the report.

173 sick: Swedish school suffers vomiting bug outbreak

As the annual winter vomiting bug season starts to kick in it’s the Tofta high school in the south which is bearing the brunt of it so far. 

vomit.2In total 173 people who attend or work at the school have been affected by the bug. Even the headmaster hasn’t been spared.

“It struck last Friday but now I’m back at work,” headmaster Tobias Fahlén told the Expressen newspaper.

Parents reported that the bug began to take hold on Friday, with many stating that their children began vomiting uncontrollably. Several have asked the school to investigate the outbreak which has led to deserted classrooms.

As a result the school has now got in contact with the disease control centre in nearby Malmö. The centre advised the school to do some extra cleaning in the toilets and school kitchen to help combat the vomiting bug.

An epidemiologist with the disease control centre who is working with the school said it was most likely a vomiting bug that was ravaging the school, and not food poisioning as some parents had suspected.

We’re all hosts on a viral planet: Viruses help keep the gut healthy

Drunken graduate student discussions about the role of viruses in human development have taken on new importance now that researchers studying mice have shown that a virus can help maintain and restore a healthy gut in much the same way that friendly bacteria do.

kellysheroes2t1oddballThe work “shows for the first time that a virus can functionally substitute for a bacterium and provide beneficial effects,” says Julie Pfeiffer, a virologist at the University of Texas Southwestern Medical Center in Dallas who was not involved with the study. “It’s shocking.”

Our bodies are mostly microbes, with each of us hosting a hundred trillion bacteria as our so-called microbiome. These bacteria appear to play a role in everything from our weight to our allergies. But viruses also lurk in and around those bacteria—and they vastly outnumber the microbes.

Like the microbiome, this “virome” may be important for human health. One recent study, for example, found that viruses that are abundant in saliva may weed out harmful bacteria. Kenneth Cadwell, a virologist at New York University School of Medicine in New York City, wanted to know what viruses in the gut might be doing. In particular, he was interested in a group called noroviruses. Although they are notorious for causing epidemics of diarrhea on cruise ships and disease in lab mouse colonies, some noroviruses infect mice with no ill effects.

Reminds of this scene from 1978’s Animal house, but I could only find the clip in this other language.