sneezeAn otherwise balanced review of selected aspects of Ebolavirus transmission falls apart when the authors hypothesize that ‘Ebola viruses have the potential to be respiratory pathogens with primary respiratory spread.’

The idea that Ebolavirus might become transmitted by the respiratory route was suggested last year by Michael Osterholm in a Times OpEd. That idea was widely criticized by many virologists, including this writer.  Now he has recruited 20 other authors, including Ebola virologists, in an attempt to lend legitimacy to his hypothesis. Unfortunately the new article adds no new evidence to support this view.

In the last section of the review article the authors admit that they have no evidence for respiratory transmission of Ebolavirus:

It is very likely that at least some degree of Ebola virus transmission currently occurs via infectious aerosols generated from the gastrointestinal tract, the respiratory tract, or medical procedures, although this has been difficult to definitively demonstrate or rule out, since those exposed to infectious aerosols also are most likely to be in close proximity to and in direct contact with an infected case.

It is possible that some short-distance transmission of Ebolavirus occurs through the air. But claiming that it is ‘very likely’ to be taking place is an overstatement considering the lack of evidence. As might be expected, ‘very likely’ is exactly the phrase picked up by the Washington Post.

I find the lack of critical thinking in the following paragraph even more disturbing:

To date, investigators have not identified respiratory spread (either via large droplets or small-particle aerosols) of Ebola viruses among humans. This could be because such transmission does not occur or because such transmission has not been recognized, since the number of studies that have carefully examined transmission patterns is small. Despite the lack of supportive epidemiological data, a key additional question to ask is whether primary pulmonary infections and respiratory transmission of Ebola viruses could be a potential scenario for the future.

Why is the possibility of respiratory transmission of Ebolaviruses a ‘key additional question’ when there has been no evidence for it to date? To make matters worse, the authors have now moved from short-range transmission of the virus by droplets, to full-blown respiratory aerosol transmission.

The authors present a list of reasons why they think Ebolavirus could go airborne, including: isolation of Ebolaviruses from saliva; presence of viral particles in pulmonary alveoli on human autopsies; and cough, which can generate aerosols, can be a symptom of Ebolavirus disease. The authors conclude that because of these properties, the virus would not have to change very much to be transmitted by aerosols.

I would conclude the opposite from this list of what Ebolavirus can do: there is clearly a substantial block to respiratory transmission that the virus cannot overcome. Perhaps the virus is not stable enough in respiratory aerosols, or there are not enough infectious viruses in aerosols to transmit infection from human to human. Overcoming these blocks might simply not be biologically possible for Ebolavirus. A thoughtful discussion of these issues is glaringly absent in the review.

The conclusion that Ebolavirus is  ‘close’ to becoming a full-blown respiratory pathogen reveals how little we understand about the genetic requirements for virus transmission. In fact the authors cannot have any idea how ‘close’ Ebolavirus is to spreading long distances through the air.

It is always difficult to predict what viruses will or will not do. Instead, virologists observe what viruses have done in the past, and use that information to guide their thinking. If we ask the simple question, has any human virus ever changed its mode of transmission, the answer is no. We have been studying viruses for over 100 years, and we’ve never seen a human virus change the way it is transmitted. There is no evidence to believe that Ebolavirus is any different.

Viruses are masters of evolution, but apparently one item lacking from their repertoire is the ability to change the way that they are transmitted.

Such unfounded speculation would largely be ignored if the paper were read only by microbiologists. But Ebolavirus is always news and even speculation does not go unnoticed. The Washington Post seems to think that this review article is a big deal. Here is their headline: Limited airborne transmission of Ebola is ‘very likely’ new analysis says.

Gary Kobinger, one of the authors, told the Washington Post that ‘we hope that this review will stimulate interest and motivate more support and more scientists to join in and help address gaps in our knowledge on transmission of Ebola’. Such hope is unrealistic, because few can work on this virus, which requires the highest levels of biological containment, a BSL-4 laboratory.

I wonder if Osterholm endorses Kobinger’s hopes. After all, he opposed studies of influenza virus transmission in ferrets, claiming that they are too dangerous. And the current moratorium on research that would help us understand aerosol transmission of influenza viruses is a direct result of objections by Osterholm and his colleagues about this type of work. The genetic experiments that are clearly needed to understand the limitations of Ebolavirus transmission would never be permitted, at least not with United States research dollars.

The gaps in our understanding of virus transmission are considerable. If virologists are not able to carry out the necessary experiments to fill these gaps, all we will have is rampant and unproductive speculation.

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paramyxovirus fusionThe entry of enveloped viruses into cells begins when the membrane that surrounds these virus particles fuse with a cell membrane. The process of virus-cell fusion must be tightly regulated, to make sure it happens in the right cells. The fusion activity of measles viruses isolated from the brains of AIDS patients is not properly regulated, which might explain why these viruses cause disease in the central nervous system.

Measles virus particles bind to cell surface receptors via the viral glycoprotein HN (illustrated). Once the viral and cell membranes have been brought together by this receptor-ligand interaction, fusion is induced by a second viral glycoprotein called F, and the viral RNA is released into the cell cytoplasm. The N-terminal 20 amino acids of F protein are highly hydrophobic and form a region called the fusion peptide that inserts into target membranes to initiate fusion. Because F-protein-mediated fusion can occur at neutral pH, it must be controlled, to ensure that virus particles fuse with only the appropriate cell, and to prevent aggregation of newly made virions. The fusion peptide of F is normally hidden, and conformational changes in the protein thrust the it toward the cell membrane (illustrated). These conformational changes in the F protein, which expose the fusion peptide, are thought to occur upon binding of HN protein to its cellular receptor.

During a recent outbreak of measles in South Africa, several AIDS patients died when measles virus entered and replicated in their central nervous systems. Measles virus normally enters via the respiratory route, establishes a viremia (and the characteristic rash) and is cleared within two weeks. The virus is known to enter the brain in up to half of infected patients, but without serious sequelae. The measles inclusion body encephalitis observed in these AIDS patients typically occurs in immunosuppressed individuals several months after infection with measles virus.

Measles virus isolated postmortem from these two individuals had a single amino acid change in the F glycoprotein, from leucine to tryptophan at position 454. This single amino acid change allowed viruses to fuse with cell membranes without having to first bind a cellular receptor via the HN glycoprotein. In other words, the normal mechanism for regulating measles virus fusion – binding a cell receptor – was bypassed in these viruses. This unusual property might have allowed measles virus to spread throughout the central nervous system, causing lethal disease.

How did these mutant viruses arise in the AIDS patients? Because these individuals had impaired immunity as a result of HIV-1 infection, they were not able to clear the virus in the usual two weeks. As a consequence, the virus replicated for several months. During this time, the mutation might have arisen that allowed unregulated fusion of virus and cell, leading to unchecked replication in the brain. Alternatively, the mutation might have been present in virus that infected these individuals, and was selected in the central nervous system.

An interesting question is whether these neurotropic measles viruses can be transmitted by aerosol between hosts – a rather unsettling scenario. Fortunately, we do have a measles virus vaccine that effectively prevents infection, even with these mutant viruses.

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On episode #324 of the science show This Week in Virology, Lee joins the TWiV team to discuss the value of post-doctoral training, and how a cellular microRNA assists in the replication of hepatitis C virus.

You can find TWiV #324 at www.twiv.tv.

What does transfection mean?

12 February 2015

infectious poliovirus dnaI have always had a problem with the use of the word transfection to mean anything other than the introduction of viral DNA into cells (illustrated for poliovirus). An examination of the origins of the word suggests that such use might be acceptable.

The introduction of foreign DNA into cells is called DNA-mediated transformation to distinguish it from the oncogenic transformation of cells caused by tumor viruses and other insults. The term transfection (transformation-infection) was coined to describe the production of infectious virus after transformation of cells by viral DNA, first demonstrated with bacteriophage lambda. Unfortunately, transfection is now routinely used to describe the introduction of any DNA or RNA into cells.

If you view the English language as a dynamic means of communication that continually evolves and provides words with new meanings, then this incorrect use of transfection probably does not bother you. But scientists must be precise in their use of language, otherwise their ability to communicate will be impaired. This is why the use of transfection to mean anything other than introduction of viral DNA into cells is a bad idea. I do understand that transfection is much easier to write or speak than DNA-mediated transformation, but surely that cannot be an excuse for warping a word’s meaning.

The misuse of transfection bothers me so much, that whenever I see the term, I inspect the usage to see if it is incorrect. Recently after seeing another improper use of the word, I decided to look up its roots. What I found made me reconsider my angst about transfection.

The word ‘trans’ can mean across or through. The word infection, from which the -fection in transfection is derived, comes from the Latin verb inficere: from in (into) + facere (put, do). From this analysis we can determine that transfection means across-put. That is not a bad definition of what transfection has come to mean: put DNA across a membrane into the cell.

I am certainly not a student of etymology, but it seems to me that without knowing it, those who used transfection in the wrong way were actually correct in their usage. I no longer need fret about how transfection is used!

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Jason Roberts, a virologist at the Victorian Infectious Disease Reference Laboratory in Melbourne, Australia, creates three-dimensional simulations of viruses showing how the molecules that make up the capsid and genome might move in very short periods of time. I visited Jason in his laboratory at the newly constructed Peter Doherty Institute, to learn how he develops these simulations. Then I toured the Peak Computing Facility, which houses the supercomputer that calculates Jason’s simulations.

 

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On episode #323 of the science show This Week in Virology, the family TWiVidae discuss changes in the human fecal virome associated with Crohn’s disease and ulcerative colitis.

You can find TWiV #323 at www.twiv.tv.

prion conversionThe human prion disease, Creutzfeld-Jacob, is diagnosed by a variety of criteria, including clinical features, electroencephalograms, and magnetic resonance imaging. Until recently there was no non-invasive assay to detect PrPSc, the only specific marker for the disease. This challenge has been overcome using amplification procedures to detect Creutzfeldt-Jakob prions in nasal brushings and in urine.

These assays utilize two different methods for amplifying the quantity of prions in vitro. In real-time quaking-induced conversion, PrPC (produced in E. coli) is mixed with a small amount of PrPSc. The mixtures are subjected to cycles of shaking and rest at 42°C for 55-90 hours, which leads to the formation of amyloid fibrils that can be detected by fluorescence. The assay can detect femtogram levels of PrPSc in brain homogenates from humans with Creutzfeld-Jacob disease. In protein misfolding cyclic amplification, samples are incubated for 30 minutes at 37°- 40°C, followed by a pulse of sonication, and this cycle is repeated 96 times. Prions are detected by western blot analysis after treatment with proteinase K. This process can detect a single oligomeric PrPSC.

Two non-invasive assays using these amplification approaches were developed. The first is a nasal-brushing procedure to sample the olfactory epithelium, where PrPSc is known to accumulate in patients with the disease. The real-time quaking-induced conversion assay was positive in 30 of 31 patients with Creutzfeld-Jacob disease, and negative in 43 of 43 healthy controls (a sensitivity of 97%). Furthermore, nasal brushings gave stronger and faster positive results than cerebrospinal fluid in this assay. The high concentrations of PrPSc detected in nasal brushings suggest that prions can contaminate nasal discharge of patients with the disease, a possible source of iatrogenic transmission, which has implications for infection control.

Protein misfolding cyclic amplification was used to assay for the presence of PrPSc in the urine of patients with variant Creutzfeldt-Jakob disease (caused by ingestion of beef from cows with bovine spongiform encephalopathy), which had been previously shown to contain prions. PrPSc was detected in 13 of 14 urine samples from patients with the disease, but not in 224 urine samples from healthy controls and patients with other neurologic diseases, including other TSEs. The estimated concentration of PrPSc in urine was 40-100 oligomeric particles per ml.

Because Creutzfeldt-Jakob disease is so rare, any assay for the disease must have near-perfect specificity. A problem with both cycling assays is that PrPC converts into oligomers and fibrils in the absence of PrPSc. Additional work is needed to address this problem. Nevertheless it is possible that these assays could one day lead to earlier diagnosis and treatments, if the latter become available.

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On episode #322 of the science show This Week in Virology, the TWiVodes answer listener email about hantaviruses, antivirals, H1N1 vaccine and narcolepsy, credibility of peer review, Bourbon virus, influenza vaccine, careers in virology, and much more.

You can find TWiV #322 at www.twiv.tv.

prion conversionIf the reader does not believe that viroids and satellites are distinctive, then surely prions, infectious agents composed only of protein, must impress.

The question of whether infectious agents exist without genomes arose with the discovery and characterization of infectious agents associated with a group of diseases called transmissible spongiform encephalopathies (TSEs). These diseases are rare, but always fatal, neurodegenerative disorders that afflict humans and other mammals. They are characterized by long incubation periods, spongiform changes in the brain associated with loss of neurons, and the absence of host responses. TSEs are caused by infectious proteins called prions.

The first TSE recognized was scrapie, so called because infected sheep tend to scrape their bodies on fences so much that they rub themselves raw. Scrapie has been recognized as a disease of European sheep for more than 250 years. It is endemic in some countries, for example, the United Kingdom, where it affects 0.5 to 1% of the sheep population each year.

Sheep farmers discovered that animals from affected herds could pass the disease to a scrapie-free herd, implicating an infectious agent. Infectivity from extracts of scrapie-affected sheep brains was shown to pass through filters with pores small enough to retain everything but viruses. As early as 1966, scrapie infectivity was shown to be considerably more resistant than that of most viruses to ultraviolet (UV) and ionizing radiation. Other TSE agents exhibit similar UV resistance. On the basis of this relative resistance to UV irradiation, some investigators argued that TSE agents are viruses well shielded from irradiation, whereas others claimed that TSE agents have little or no nucleic acids.

Several lines of evidence indicated that human spongiform encephalopathies might be caused by an infectious agent. Carleton Gajdusek and colleagues studied the disease kuru, found in the Fore people of New Guinea. This disease is characterized by cerebellar ataxia (defective motion or gait) without loss of cognitive functions. Kuru spread among women and children as a result of ritual cannibalism of the brains of deceased relatives. When cannibalism stopped in the late 1950s, kuru disappeared. Others observed that lesions in the brains of humans with kuru were similar to lesions in the brains of animals with scrapie. It was soon demonstrated that kuru and other human TSEs can be transmitted to chimpanzees and laboratory animals.

Human spongiform encephalopathies are placed into three groups: infectious, familial or genetic, and sporadic, distinguished by how the disease is acquired initially. An infectious (or transmissible) spongiform encephalopathy is exemplified by kuru and iatrogenic spread of disease to healthy individuals by transplantation of infected corneas, the use of purified hormones, or transfusion with blood from patients with the TSE Creutzfeldt-Jakob disease (CJD). Over 400 cases of iatrogenic Creutzfeldt-Jakob disease have been reported worldwide. The epidemic spread of bovine spongiform encephalopathy (mad cow disease, see below) among cattle in Britain can be ascribed to the practice of feeding processed animal by-products to cattle as a protein supplement. Similarly, the new human disease, variant CJD, arose after consumption of beef from diseased cattle. Sporadic CJD is a disease affecting one to five per million annually, usually late in life (with a peak at 68 years). As the name indicates, the disease appears with no warning or epidemiological indications. Kuru may have been originally established in the small population of Fore people in New Guinea when the brain of an individual with sporadic CJD was eaten. Familial spongiform encephalopathy is associated with an autosomal dominant mutation in the prnp gene. Together familial and sporadic forms of prion disease account for ~99% of all cases.

Clinical signs of infection commonly include cerebellar ataxia, memory loss, visual changes, dementia, and akinetic mutism, with death occurring after months or years. Once the infectious agent is in the central nervous system, the characteristic pathology includes severe astrocytosis, vacuolization (hence the term spongiform), and loss of neurons. There are no inflammatory, antibody, or cellular immune responses.

The unconventional physical attributes and slow infection pattern originally prompted many to argue that TSE agents are not viruses at all. In 1967 it was suggested that scrapie could be caused by a host protein, not by a nucleic acid-carrying virus.

An important breakthrough occurred in 1981, when characteristic fibrillar protein aggregates were visualized in infected brains. These aggregates could be concentrated by centrifugation and remained infectious. Stanley Prusiner and colleagues isolated a protein with unusual properties from scrapie-infected tissue. This protein is insoluble and relatively resistant to proteases. He named the scrapie infectious agent a prion, from the words protein and infectious.

Prusiner’s unconventional proposal was that an altered form of a normal cellular protein, called PrPC, causes the fatal encephalopathy characteristic of scrapie. This controversial protein-only hypothesis caused a firestorm among those who study infectious disease. The hypothesis was that the essential pathogenic component is the host-encoded PrPC protein with an altered conformation, called PrPsc (“PrP-scrapie”). Furthermore, in the simplest case, PrPSc was proposed to have the property of converting normal PrPC protein into more copies of the pathogenic form (illustrated). In recognition of his work on prions, Prusiner was awarded the Nobel Prize in physiology or medicine in 1997.

Sequence analysis of this protein led to the identification of the prnp gene, which is highly conserved in the genomes of many mammals, including humans. Expression of the prnp gene is now known to be essential for the pathogenesis of TSEs. The prnp gene encodes a 35-kDa membrane-associated neuronal glycoprotein, PrPC. The function of this protein has been difficult to determine because mice lacking both copies of the prnp gene develop normally and have few obvious defects. However, these mice are resistant to TSE infection, showing that PrPC is essential for prion propagation.

The discovery of the prnp gene has helped explain the basis of familial TSE diseases such as Creutzfeldt-Jakob disease, Gerstmann-Straussler-Scheinker disease, and fatal familial insomnia. Gerstmann-Straussler-Scheinker disease is associated with a change at PrPC amino acid 102 from proline to leucine. Introduction of this amino acid change into mice gives rise to a spontaneous neurodegenerative disease characteristic of a TSE. Familial Creutzfeldt-Jakob disease may be associated with an insertion of 144 base pairs at codon 53, or changes at amino acids 129, 178, or 200. In fatal familial insomnia, adults develop a progressive sleep disorder and typically die within one year. Development of this disease is strongly linked to the D178N amino acid change.

In the mid 1980s, a new disease appeared in cows in the United Kingdom: bovine spongiform encephalopathy, also called mad cow disease. It is believed to have been transmitted to cows by feeding them meat and bone meal, a high protein supplement prepared from the offal of sheep, cattle, pigs, and chicken. In the late 1970s the method of preparation of meat and bone meal was changed, resulting in material with a higher fat content. It is believed that this change allowed prions, from either a diseased sheep or cow, to retain infectivity and pass on to cattle. Before the disease was recognized in 1985, it was amplified by feeding cows the remains of infected bovine tissues: the incubation period for bovine spongiform encephalopathy is 5 years, but disease was not observed because most cattle are slaughtered between 2-3 years of age. Three years later, as the number of cases of mad cow disease increased, a ban on the use of meat and bone meal was put in place, a practice that together with culling infected cattle has stopped the epidemic. Over 180,000 cattle, mostly dairy cows, died of bovine spongiform encephalopathy from 1986-2000.

Cases of variant Creutzfeld-Jakob disease, a new TSE of humans, began to appear in 1994 in Great Britain. These were characterized by a lower mean age of the patients (26 years), longer duration of illness, and differences in other clinical and pathological characteristics. The results of epidemiologic and experimental studies indicate that variant Creutzfeld-Jakob disease is caused by prions transmitted by the consumption of cattle with bovine spongiform encephalopathy. As of 2011 there had been 175 cases of variant Creutzfeld-Jakob disease in the United Kingdom, and 215 globally.

Bovine spongiform encephalopathy continues to be detected in cattle. As of April 2012, 4 cases have been identified in the United States and 19 in Canada. These cases may arise sporadically, or through consumption of contaminated feed. Because cattle are slaughtered before disease symptoms are evident, there is concern that variant Creutzfeldt-Jakob might increase as contaminated meat enters the food supply. These concerns are being addressed by imposing bans on animal protein-containing feed, and increased surveillance of cows for the disease, for which diagnostic tests are being developed.

Chronic wasting disease is a transmissible spongiform encephalopathy of cervids such as deer, elk, and moose. It is the only known TSE to occur in free-ranging animals. The disease has been reported in the United States, Canada, and South Korea. In captive herds in the US and Canada up to 90% of mule deer and 60% of elk are infected, and the incidence in wild cervids is as high as 15%. Hunters are advised not to shoot or consume an elk or deer that is acting abnormally or appears to be sick, to avoid the brain and spinal cord when field dressing game, and not to consume brain, spinal cord, eyes, spleen, or lymph nodes. No case of transmission of chronic wasting disease prions to deer hunters has yet been reported.

It is not known how the disease is spread among cervids, but transmission by grass contaminated with saliva and feces is one possibility. When deer are fed prions they excrete them in the feces before developing clinical signs of infection, and prions can also be detected in deer saliva. In the laboratory, brain homogenates from infected deer can transmit the disease to cows. A concern is that prions of chronic wasting disease could be transmitted to cows grazing in pastures contaminated by cervids.

Since prions were discovered it has become clear that they cause a wider spectrum of neurodegenerative diseases. For example, the amyloid fibrils in Alzheimer’s disease contain the amyloid-beta peptide that is processed from the amyloid precursor protein; familial disease is caused by mutations in the gene for this protein. Mutations in the tau gene are responsible for heritable tauopathies including familial frontotemporal dementia and inherited progressive supranuclear palsy. Self-propagating tau aggregates pass from cell to cell. The prion-like spread of misfolded alpha-synuclein is believed to be involved in Parkinson’s disease. In these cases there is good evidence that the causative protein, like PrPSc, adopts a conformation that becomes self-propagating.

Despite the involvement of prions in human neurological diseases, in other organisms such proteins are not pathogenic but rather impart diverse functions through templated conformational change of a normal cellular protein. Such prions have been described in fungi where they do not form infectious particles and do not spread from cell to cell. These proteins change conformation in response to an environmental stimulus and acquire a new, beneficial function. An example is the Saccharomyces cerevisiae Ure2p protein, which normally is a nitrogen catabolite repressor when cells are grown in the presence of a rich source of nitrogen. In the aggregated prion state, called [URE3], the protein allows growth on poor nitrogen sources. These findings prompt the question of whether the conversion of PrPC to PrPSC once had a beneficial function that became pathogenic. If so, identifying that function, and how it was usurped, will be important for understanding the pathogenesis of transmissible spongiform encephalopathies.

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TWiV 321: aTRIP and a pause

25 January 2015

On episode #321 of the science show This Week in Virology, Paul Duprex joins the TWiV team to discuss the current moratorium on viral research to alter transmission, range and resistance, infectivity and immunity, and pathogenesis.

You can find TWiV #321 at www.twiv.tv.