On episode #303 of the science show This Week in Virology, the TWiV team discusses transmission of Ebola virus, and inhibition of Borna disease virus replication by viral DNA in the ground squirrel genome.
You can find TWiV #303 at www.twiv.tv.
21 September 2014
18 September 2014
In a recent New York Times OpEd entitled What We’re Afraid to Say About Ebola, Michael Osterholm wonders whether Ebola virus could go airborne:
You can now get Ebola only through direct contact with bodily fluids. If certain mutations occurred, it would mean that just breathing would put one at risk of contracting Ebola. Infections could spread quickly to every part of the globe, as the H1N1 influenza virus did in 2009, after its birth in Mexico.
Is there any truth to what Osterholm is saying?
Let’s start with his discussion of Ebola virus mutation:
But viruses like Ebola are notoriously sloppy in replicating, meaning the virus entering one person may be genetically different from the virus entering the next. The current Ebola virus’s hyper-evolution is unprecedented; there has been more human-to-human transmission in the past four months than most likely occurred in the last 500 to 1,000 years.
When viruses enter a cell, they make copies of their genetic information to assemble new virus particles. Viruses such as Ebola virus, which have genetic information in the form of RNA (not DNA as in other organisms), are notoriously bad at copying their genome. The viral enzyme that copies the RNA makes many errors, perhaps as many as one or two each time the viral genome is reproduced. There is no question that RNA viruses are the masters of mutation. This fact is in part why we need a new influenza virus vaccine every few years.
The more hosts infected by a virus, the more mutations will arise. Not all of these mutations will find their way into infectious virus particles because they cause lethal defects. But Osterholm’s statement that the evolution of Ebola virus is ‘unprecedented’ is simply not correct. It is only what we know. The virus was only discovered to infect humans in 1976, but it surely infected humans long before that. Furthermore, the virus has been replicating, probably for millions of years, in an animal reservoir, possibly bats. There has been ample opportunity for the virus to undergo mutation.
More problematic is Osterholm’s assumption that mutation of Ebola virus will give rise to viruses that can transmit via the airborne route:
If certain mutations occurred, it would mean that just breathing would put one at risk of contracting Ebola. Infections could spread quickly to every part of the globe, as the H1N1 influenza virus did in 2009, after its birth in Mexico.
The key phrase here is ‘certain mutations’. We simply don’t know how many mutations, in which viral genes, would be necessary to enable airborne transmission of Ebola virus, or if such mutations would even be compatible with the ability of the virus to propagate. What allows a virus to be transmitted through the air has until recently been unknown. We can’t simply compare viruses that do transmit via aerosols (e.g. influenza virus) with viruses that do not (e.g. HIV-1) because they are too different to allow meaningful conclusions.
One approach to this conundrum would be to take a virus that does not transmit among mammals by aerosols – such as avian influenza H5N1 virus – and endow it with that property. This experiment was done by Fouchier and Kawaoka several years ago, and revealed that multiple amino acid changes are required to allow airborne transmission of H5N1 virus among ferrets. These experiments were met with a storm of protest from individuals – among them Michael Osterholm – who thought they were too dangerous. Do you want us to think about airborne transmission, and do experiments to understand it – or not?
The other important message from the Fouchier-Kawaoka ferret experiments is that the H5N1 virus that could transmit through the air had lost its ability to kill. The message is clear: gain of function (airborne transmission) is accompanied by loss of function (virulence).
When it comes to viruses, it is always difficult to predict what they can or cannot do. It is instructive, however, to see what viruses have done in the past, and use that information to guide our thinking. Therefore we can ask: 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.
HIV-1 has infected millions of humans since the early 1900s. It is still transmitted among humans by introduction of the virus into the body by sex, contaminated needles, or during childbirth.
Hepatitis C virus has infected millions of humans since its discovery in the 1980s. It is still transmitted among humans by introduction of the virus into the body by contaminated needles, blood, and during birth.
There is no reason to believe that Ebola virus is any different from any of the viruses that infect humans and have not changed the way that they are spread.
I am fully aware that we can never rule out what a virus might or might not do. But the likelihood that Ebola virus will go airborne is so remote that we should not use it to frighten people. We need to focus on stopping the epidemic, which in itself is a huge job.
14 September 2014
9 September 2014
During the winter of 1962 in California, a new virus was isolated from the oropharynx of 4 children who had been hospitalized with respiratory disease that included pneumonia and bronchiolitis. On the basis of its physical, chemical, and biological properties, the virus was classified as an enterovirus in the picornavirus family. Subsequently named enterovirus D68, it has been rarely reported in the United States (there were 79 isolations from 2009-2013). Towards the end of August 2014, an outbreak of severe respiratory disease associated with EV-D68 emerged in Kansas and Illinois.
Hospitals in Kansas City, Missouri, and Chicago, Illinois reported to the CDC an increase in the number of patients hospitalized with severe respiratory illness. EV-D68 was subsequently identified by polymerase chain reaction and nucleotide sequencing in 19/22 and 11/14 nasopharyngeal specimens from Kansas City and Chicago, respectively. Median ages of the patients were 4 and 5 years in the two cities, and most were admitted to the pediatric intensive care units due to respiratory distress. Other states have reported increases in cases of severe respiratory illness, and these are being investigated at CDC to determine if they are also associated with EV-D68.
There is no vaccine to prevent EV-D68 infection, nor is antiviral therapy available to treat infected patients. Current treatment is supportive to assist breathing; in a healthy individual the infection will resolve within a week. In the current outbreak no fatalities have been reported.
EV-D68 has been previously associated with mild to severe respiratory illness and is known to cause clusters of infections. It is not clear why there has been a sudden increase in the number of cases in the US. According to Mark Pallansch, Director of the Division of Viral Diseases at CDC, “our ability to find and detect the virus has improved to the point where we may now be recognizing more frequently what has always occurred in the past. So a lot of these techniques are now being applied more routinely both at the CDC but also at state health departments.” (Source: NPR).
I am sure that the nucleotide sequence of the EV-D68 virus isolated from these patients will reveal differences with previous strains. However whether or not those changes have anything to do with the increased number of isolations in the US will be very difficult to determine, especially as there is no animal model for EV-D68 respiratory disease.
Although how EV-D68 is transmitted has not been well studied, the virus can be detected in respiratory secretions (saliva, nasal mucus, sputum) and is therefore likely to spread from person to person by coughing, sneezing, or touching contaminated surfaces. The virus has been isolated from some of the children in California with acute flaccid paralysis, and there is at least one report of its association with central nervous system disease. In this case viral nucleic acids were detected in the cerebrospinal fluid. EV-D68 probably does not replicate in the human intestinal tract because the virus is inactivated by low pH.
Readers might wonder why a virus that causes respiratory illness is called an enterovirus. This nomenclature is largely historical: poliovirus, which replicates in the enteric tract, was the prototype member of this genus. Other viruses, including Coxsackieviruses and echoviruses, were added to the genus based on their physical and chemical properties. However soon it became apparent that many of these viruses could also replicate in the respiratory tract. Years later the rhinoviruses, which do not replicate in the enteric tract, were added to the enterovirus genus based on nucleotide sequence comparisons. While it was decided to keep the name ‘enterovirus’ for this group of viruses, it is certainly confusing and I would argue that it should be replaced by a more descriptive name.
7 September 2014
On episode #301 of the science show This Week in Virology, Vincent travels to the International Congress of Virology in Montreal and speaks with Carla Saleh and Curtis Suttle about their work on RNA interference and antiviral defense in fruit flies, and viruses in the sea, the greatest biodiversity on Earth.
You can find TWiV #301 at www.twiv.tv.
6 September 2014
Since the beginning of the AIDS epidemic, an estimated 75 million people have been infected with HIV. Only one person, Timothy Ray Brown, has ever been cured of infection.
Brown was diagnosed with HIV while living in Berlin in 1995, and was treated with anti-retroviral drugs for more than ten years. In 2007 he was diagnosed with acute myeloid leukemia. When the disease did not respond to chemotherapy, Brown underwent stem cell transplantation, which involves treatment with cytotoxic drugs and whole-body irradiation to destroy leukemic and immune cells, followed by administration of donor stem cells to restore the immune system. When his leukemia relapsed, Brown was subjected to a second stem cell transplant.
The entry of HIV-1 into lymphocytes requires two cellular proteins, the receptor CD4, and a co-receptor, either CXCR4 or CCR5. Individuals who carry a mutation in the gene encoding CCR5, called delta 32, are resistant to HIV-1 infection. This information prompted Brown’s Berlin physician to screen 62 individuals to identify a stem cell donor who carried a homozygous CCR5∆32 mutation. Peripheral blood stem cells from the same donor were used for both transplants.
Despite enduring complications and undergoing two transplants, Brown’s treatment was a success: he was cured both of his leukemia and HIV infection. Even though he had stopped taking antiviral drugs, there was no evidence of the virus in his blood following his treatment, and his immune system gradually recovered. Follow-up studies in 2011, including biopsies from his brain, intestine, and other organs, showed no signs of HIV RNA or DNA, and also provided evidence for the replacement of long-lived host tissue cells with donor-derived cells. Today Brown remains HIV-1 free.
Although Brown’s cure is somewhat of a medical miracle, and by no means a practical road map for treating AIDS, the example of the Berlin patient has galvanized research efforts and continues to inspire hope that a simpler and more general cure for infection may someday be achieved. Clinical trials have been conducted to test a variety of strategies in which CD4+ T or stem cells are obtained from a patient, the CCR5 gene is either mutated or its translation blocked by RNA interference, and then the resulting virus-resistant cells are returned to the patient. In one case zinc finger nucleases were used to delete the CCR5 gene in a patient’s cells, a procedure that we discussed in TWiV #278.
31 August 2014
Recording together for the first time, the hosts of the science show This Week in Virology celebrate their 300th recording at the American Society for Microbiology headquarters in Washington, DC, where Vincent speaks with Dickson, Alan, Rich, and Kathy about their careers in science.
You can find TWiV #300 at www.twiv.tv.
29 August 2014
Antigenic variation is a hallmark of influenza virus that allows the virus to evade host defenses. Consequently influenza vaccines need to be reformulated frequently to keep up with changing viruses. In contrast, antigenic variation is not a hallmark of poliovirus – the same poliovirus vaccines have been used for nearly 60 years to control infections by this virus. An exception is a poliovirus type 1 that caused a 2010 outbreak in the Republic of Congo.
The 2010 outbreak (445 paralytic cases) was unusual because the case fatality ratio of 47% was higher than typically observed (usually less than 10% of patients with confirmed disease die). The first clue that something was different in this outbreak was the finding that sera from some of the fatal cases failed to effectively block (neutralize) infection of cells by the strain of poliovirus isolated during this outbreak (the strain is called PV-RC2010). The same sera effectively neutralized the three Sabin vaccine viruses as well as wild type 1 polioviruses isolated from previous outbreaks. Therefore gaps in vaccination coverage were solely not responsible for this outbreak.
Examination of the nucleotide sequence of the genome of type I polioviruses isolated from 12 fatal cases revealed two amino acid changes within a site on surface of the viral capsid that is bound by neutralizing antibodies (illustration). The sequence of this site, called 2a, was changed from ser-ala-ala-leu to pro-ala-asp-leu. This particular combination of amino acid substitutions has never been seen before in poliovirus. Virus PV-RC2010, which also contains these two amino acid mutations, is completely resistant to neutralization with monoclonal antibodies that recognize antigenic site 2 (monoclonal antibodies recognize a single epitope, as opposed polyclonal antibodies which is a mixture of antibodies that recognize many epitopes. The antibodies in serum are typically polyclonal).
Poliovirus neutralization titers were determined using sera from Gabonese and German individuals who had been immunized with Sabin vaccine. These sera effectively neutralized the type I strain of Sabin poliovirus, as well as type 1 polioviruses isolated from recent outbreaks. However the sera had substantially lower neutralization activity against PV-RC2010. From 15-29% of these individuals would be considered not to be protected from infection with this strain.
Nucleotide sequence analysis of PV-RC2010 reveals that it is related to a poliovirus strain isolated in Angola in 2009, the year before the Republic of Congo outbreak. The Angolan virus had just one of the two amino acid changes in antigenic site 2a found in PV-RC2010.
It is possible that the relative resistance of the polioviruses to antibody neutralization might have been an important contributor to the high virulence observed during the Republic of Congo outbreak. The reduced ability of serum antibodies to neutralize virus would have lead to higher virus in the blood and a greater chance of entering the central nervous system. Another factor could also be that many of the cases of poliomyelitis were in adults, in which the disease is known to be more severe.
An important question is whether poliovirus strains such as PV-RC2010 pose a global threat. Typically the fitness of antigenically variant viruses is not the same as wild type, and therefore such viruses are not likely to spread in well immunized populations. Today some parts of the world have incomplete poliovirus immunization coverage, which together with the reduced circulation of wild type polioviruses leads to reduced population immunity. Such a situation could lead to the evolution of antigenic variants. This situation occurred in Finland in 1984, when an outbreak caused by type 3 poliovirus took place. The responsible strains were antigenic variants that evolved due to use of a sub-optimal poliovirus vaccine in that country.
The poliovirus outbreaks in the Republic of Congo and Finland were stopped by immunization with poliovirus vaccines, which boosted the population immunity. These experiences show that poliovirus antigenic variants such as PV-RC2010 will not cause outbreaks as long as we continue extensive immunization with poliovirus vaccines, coupled with environmental and clinical testing for the presence of such viruses.
26 August 2014
On episode #299 of the science show This Week in Virology, Vincent visits the Rocky Mountain Laboratories in Hamilton, Montana and speaks with Marshall Bloom, Sonja Best, and Byron Caughey about their work on tick-born flaviviruses, innate immunity, and prion diseases.
You can find TWiV #299 at www.twiv.tv.
24 August 2014
Many people have a new awareness of the disease known as amyotrophic lateral sclerosis, or ALS, thanks to the Ice Bucket Challenge initiated by the ALS Association. Fewer might know that retroviruses have been proposed to play a role in the development of the disease.
I previously summarized a 2008 paper on ALS in a piece called Retroviruses and amyotrophic lateral sclerosis. Sera from some ALS patients had previously been shown to contain elevated levels of reverse transcriptase, an enzyme found in retrovirus particles. In the 2008 paper, RNAs encoding this enzyme were reported in the brains of ALS patients, and their origin appears to be the human endogenous retrovirus HERV-K.
The progress made in understanding the relationship of endogenous retroviruses with ALS is summarized in a review published in August of 2014 entitled Retroviruses and amyotrophic lateral sclerosis (the paper is open access). The authors conclude:
A comprehensive study of the expression or reactivation of endogenous retroviral elements in ALS has not yet been undertaken. The literature on HERV-W involvement in ALS is difficult to interpret. Two independent reports, however, have shown increased HERV-K expression in both serum and brain tissue in ALS patients. It remains unknown if HERV-K expression is an epiphenomenon or plays a pathophysiological role in the disease.
I am pleased to participate in the Ice Bucket Challenge to help raise awareness of ALS and raise money to work on the disease.
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