On episode #275 of the science show This Week in Virology, Vincent and Rich meet up with Eugene Koonin to talk about the central role of viruses in the evolution of all life.
You can find TWiV #275 at www.twiv.tv.
9 March 2014
A new virus called Pithovirus sibericum has been isolated from 30,000 year old Siberian permafrost. It is the oldest DNA virus of eukaryotes ever isolated, showing that viruses can retain infectivity in nature for very long periods of time.
Pithovirus was isolated by inoculating cultures of the amoeba Acanthamoeba castellani with samples taken in the year 2000 from 30 meters below the surface of a late Pleistocene sediment in the Kolyma lowland region. This amoeba had been previously used to propagate other giant viruses, such as Mimivirus and Pandoravirus. Light microscopy of the cultures revealed the presence of ovoid particles which were subsequently shown by electron microscopy to resemble those of Pandoravirus. Pithovirus particles are flask-shaped and slightly larger than Pandoravirus – 1.5 microns long, 500 nm in diameter, encased by a 60 nm thick membrane. One end of the virus particle appears to be sealed with what the authors call a cork (photo). This feature, along with the shape of the virus particle, inspired the authors to name the new isolate Pithovirus, from the Greek word pithos which refers to the amphora given to Pandora. The name therefore refers both to the morphology of the virus particle and its similarity to Pandoravirus.
Although the Pithovirus particle is larger than Pandoravirus, the viral genome – which is a double-stranded molecule of DNA – is smaller, a ‘mere 610,033 base pairs’, to use the authors’ words (the Pandoravirus genome is 2.8 million base pairs in length). There are other viruses with genomes of this size packed into much smaller particles – so why is the Pithovirus particle so large? Might it have recently lost a good deal of its genome and the particle size has not yet caught up? One theory of the origin of viruses is that they originated from cells and then lost genes on their way to becoming parasitic.
We now know of viruses from two different families that have similar morphology: an amphora-like shape, an apex, and a thick electron-dense tegument covered by a lipid membrane enclosing an internal compartment. This finding should not be surprising: similar viral architectures are known to span families. The icosahedral architecture for building a particle, for example, can be found in highly diverse viral families. The question is how many viruses are built with the pithovirus/pandoravirus structure. My guess would be many, and they could contain either DNA genomes. We just need to look for them, a process, as the authors say that ‘will remain a challenging and serendipitous process’.
Despite the physical similarity with Pandoravirus, the Pithovirus genome sequence reveals that it is barely related to that virus, but more closely resembles members of the Marseillviridae, Megaviridae, and Iridoviridae. These families all contain large icosahedral viruses with DNA genomes. Only 32% of the 467 predicted Pithovirus proteins have homologs in protein databases (this number was 61% for Mimivirus and 16% for Pandoravirus). In contrast to other giant DNA viruses, the genome of Pithovirus does not encode any component of the protein synthesis machinery. However the viral genome does encode the complete machinery needed to produce mRNAs. These proteins are present in the purified Pithovirus particle. Pithovirus therefore undergoes its entire replication cycle in the cytoplasm, much like other large DNA viruses such as poxviruses.
Pithovirus is an amazing virus that hints about the yet undiscovered viral diversity that awaits discovery. Its preservation in a permafrost layer suggests that these regions might harbor a vast array of infectious organisms that could be released as these regions thaw or are subjected to exploration for mineral and oil recovery. A detailed analysis of the microbes present in these regions is clearly needed, both by the culture technique used in this paper and by metagenomic analysis, to assess whether any constitute a threat to animals.
2 March 2014
27 February 2014
Recently a number of children in California have developed a poliomyelitis-like paralysis. The cause of this paralysis is not yet known, and information about the outbreak is scarce. Here is what we know so far:
I do not have any more information on this outbreak other than what I’ve obtained from ProMedMail. I have worked on enteroviruses, including poliovirus, for over 30 years, so I thought I might speculate on what might be transpiring.
What is a polio-like illness? Acute flaccid paralysis (AFP) is the term used to describe the sudden onset of weakness in limbs. AFP can have many etiologies, including viruses, bacteria, toxins, and systemic disease. It is used by the World Health Organization to maximize the ability to detect all cases of poliovirus. Confirmation that AFP is caused by poliovirus requires demonstration that the virus is present in the infected individual.
Is poliovirus the cause? I do not believe that poliovirus is causing the paralysis of children in California. I understand that they have all been immunized against poliovirus. In addition, should immunization have failed in any of these children, it seems unlikely that wild type polioviruses would be circulating in this area. Vaccine-derived polioviruses can cause paralysis but the US has not used this type of vaccine since 2000.
What might be causing the paralysis? AFP has both infectious and non-infectious etiologies. One possibility is that a non-polio enterovirus is involved. Poliovirus is classified within the genus Enterovirus in the family Picornaviridae. Other enteroviruses besides poliovirus are known to cause paralytic disease, such as Coxsackieviruses, echoviruses, and many enteroviruses including types 70, 71, 89, 90, 91,96, 99, 102, and 114.
Most enterovirus infections can be associated with different clinical syndromes besides paralysis (such as respiratory disease), and therefore diagnosis is difficult. Stool is generally the most sensitive specimen for establishing an enterovirus infection. However, the virus may no longer be present at onset of symptoms. Polio is much easier to diagnose in individuals with AFP from whom virus can be identified: paralysis is the main serious symptom caused by infection. However note that 99 out of 100 poliovirus infections are asymptomatic or present with undifferentiated viral illness. The incidence of paralytic disease caused by other enteroviruses is even lower – for example 1 in 10,000 EV71 infections are paralytic. If all of the 20 California cases are caused by enteroviruses, this means that there have been many more infections without symptoms.
In one study of non-polio AFP in India, no virus could be isolated in 70% of the cases. Enterovirus 71 was the single most prevalent serotype associated with non-polio AFP. This virus currently causes large outbreaks of hand, foot, and mouth disease throughout Asia, with many fatalities and cases of acute flaccid paralysis. EV71 is known to circulate within the United States.
What about enterovirus 68? It has been reported that EV68 has been isolated from some of the paralyzed children. This isolation does not mean that the virus has caused the paralysis. Enterovirus infections of the respiratory and gastrointestinal tracts are very common and often do not result in any signs of disease. Random samplings of healthy individuals frequently demonstrate substantial rates of enterovirus infections.
Enterovirus type 68 was first isolated in California from an individual with respiratory illness. The virus is known to cause clusters of acute respiratory disease, and there is at least one report of its association with central nervous system disease. I believe it is an unlikely cause of the paralytic cases in California based solely on the past history of the virus and the fact that other enteroviruses are more likely to cause paralysis. It is not clear to me why enterovirus 68 would evolve to become substantially more neurotropic: entering the central nervous system is a dead end because the infection cannot be transmitted to a new host.
All of the above is pure speculation based on very little data. The paralysis might not even be caused by an infection. At this point a great deal of basic epidemiology needs to be done to solve the problem – if indeed it can be solved at all. Based on its population, California would be expected to have about 75 cases of acute flaccid paralysis each year of various etiologies, suggesting that the current number of cases is not unusual or unexpected.
Update: N. Gopal Raj wrote a story last year about acute flaccid paralysis in India, which has the highest rate of non-polio AFP in the world, with 60,000 cases reported in 2011.
26 February 2014
Middle Eastern respiratory syndrome coronavirus (MERS-CoV), first identified in the fall of 2012 in a Saudi Arabian patient, has since infected over 180 individuals, causing 77 deaths. Antibodies to the virus and the viral genome have been found in dromedary camels in Jordan and Saudi Arabia, implicating those animals as the source of human infections. A new study reveals that the virus has infected camels throughout Saudi Arabia since at least 1992.
Serum, blood, and rectal and nasal swabs were collected from dromedary camels in November-December 2013 from southwestern, western, northwestern, eastern, and central regions of the Kingdom of Saudi Arabia. Of 203 serum samples, 150 (74%) were found to contain antibodies to MERS-CoV. The number of seropositive animals varied from 5% to 95% depending on location and the age of the animals (in general, seropositivity was higher in adult camels compared with young camels). Antibodies against MERS-CoV were also detected in archived serum samples from 1992 through 2010.
Polymerase chain reaction was used to detect viral nucleic acids in clinical specimens from camels. Viral nucleic acid was most frequently detected in nasal swabs; only three rectal samples were positive. More samples from juvenile camels contained viral nucleic acids (36/104, 35%) than from adults (15/98, 15%). No viral nucleic acids were detected in the blood of these animals.
Phylogenetic analysis of approximately 3 kb of viral nucleic acid sequence revealed <1% divergence from published MERS-CoV sequences.
These findings indicate that dromedary camels are a reservoir of MERS-CoV. The finding of higher seroprevalence in older camels suggests that younger animals are infected as they are introduced into herds in which the virus is circulating. Proving that infected camels are the source of human infections will require epidemiological investigations of human cases where the infection might have been acquired from camels. If camels indeed spread the virus to humans, it will be important to determine the route. As not all MERS-CoV cases have documented exposure to camels, there should be other routes of infection other than contact with camels, such as through contaminated material or person to person contact.
MERS-CoV has been circulating in dromedary camels in Saudi Arabia since 1992, but it is likely that the virus has been infecting these animals even longer. Camels do not appear to be adversely affected by MERS-CoV infection, a situation often seen when host and pathogen have co-evolved for long periods of time. Whether or not this speculation is correct will require additional work.
I spoke with two of the authors of this new study, W. Ian Lipkin and Thomas Briese, on a special episode of the science show This Week in Virology. You can find TWiV special – MERS-coronavirus in dromedary camels at www.twiv.tv. During this episode it was revealed that the investigators have propagated infectious MERS-coronavirus from nasal swabs of several dromedary camels.
23 February 2014
21 February 2014
If you are giving lectures in a course at any level, the worst practice you can engage in is to rely on notes. This behavior is problematic for several reasons. You will not properly know the material, necessitating frequent glances at your notes. The students will notice this and consider you to be unengaged and not knowledgeable. Requiring notes will more or less tie you to the lectern, or to some kind of platform at the front of the room. If you carry the notes around the room as you talk you will be perceived as confused and not authoritative with respect to the subject. Get rid of the notes.
Not relying on notes will have huge benefits for your lectures. You will be able to speak conversationally instead of in a stilted manner necessitated by looking at an outline. You can move around the room. There is no better practice than to move away from the lectern directly in front of the students. You can look them in the eye as you speak, and engage them. They will feel that you have moved among them, rather than hiding behind the lectern. Let’s face it, the lectern is a crutch – it’s a good place to hide behind if you are nervous, and clutching the sides of the podium provides false confidence. Forget about all that. I use the lectern to hold my laptop and then stay away from it for the entire lecture.
When I lecture, I move along the front and sides of the classroom, looking at the students as I talk. I only look at each slide initially to receive my cue about what I will be saying. Do not to speak to the slide – it’s the audience you are interested in. Of course there might be times when you have to walk through a complicated pathway with your laser pointer. I always look at the class while I am pointing, rather than turning to the slide and forgetting the students.
Please do not complain that you cannot remember all of the material without relying on notes. You should either study the material until you know it by heart, or do not give the lecture at all. And do not make your slides a surrogate for notes. Even worse than relying on notes is showing the class slides full of text and simply reading them. Keep the text to an absolute minimum. Use simple images and let them trigger what you have to say. You must know the material well enough to do this, otherwise you are wasting the students’ time.
It’s very important to focus on the audience; by doing so they will sense that you have a command of the material and that you are interested in teaching them. Look at them as you speak. An added benefit is that you will get many more questions this way than if you stand with your back to the audience and hide in the slides. And there is no better supplement to a great lecture than fielding questions from the audience.
There are many other elements to a great lecture, of course, such as proper delivery, having a genuine passion for the material, and arranging the elements to give a compelling story arc. No matter how hard you work on those elements, you lectures will suffer unless you lose the notes.
20 February 2014
En esta sesión hablaremos acerca de virus que codifican por una enzima llamada transcriptasa reversa. Revisaremos los ciclos de replicación de los retrovirus y los hepadnavirus, y como éstos son capaces de copiar DNA a partir de RNA, incluyendo metodos tan barrocos como la iniciación y el intercambio de templados. Tambien incluiremos una discusión acerca de la integración de DNA y de retroelementos en nuestro genoma.
10 February 2014
To the collection of avian influenza viruses known to sporadically infect humans – H5N1, H7N9, H7N2, H7N3, H7N7, H9N2, and H10N7 – we can now add H10N8, recently found in two individuals in China.
Avian influenza virus H10N8 was first detected in tracheal aspirates from a 73 year old woman who was hospitalized in November 2013 for severe respiratory illness. The patient, who died, had previously visited a live poultry market. A second infection with this virus was detected in January 2014.
Virus isolated from tracheal aspirates on day 7 of illness was named A/Jiangxi-Donghu/346/2013(H10N8). Nucleotide sequence analysis of the viral genome reveals that it is a reassortant. The HA gene most closely resembles that of a virus isolated from a duck in Hunan in 2012, while the NA gene resembles that of a virus isolated from a mallard in Korea in 2010. All six other RNA segments resemble those from circulating H9N2 viruses in China. These viruses have also provided genes for H7N9 and H5N1 viruses.
Examination of the viral protein sequences provides some clues about virulence of the virus. The HA protein sequence reveals a single basic amino acid at the cleavage site, indicating that the virus is of low pathogenicity in poultry, like H7N9 virus. The sequence in the sialic acid binding pocket of the HA protein indicates a preference for alpha-2,3 linked sialic acids, typical for avian influenza viruses (human influenza viruses prefer alpha-2,6 linked sialic acids). A lysine at amino acid 627 in the PB2 protein is known to enhance the ability of the virus to replicate at mammalian temperatures; the H10N8 virus has a mixture of lysine and glutamic acid, the residue associated with less efficient replication. The sequence of the M2 protein indicates that the virus is resistant to the antiviral adamantanes. In vitro testing indicated sensitivity to NA inhibitors Tamiflu and Relenza.
It is not known if this novel H10N8 virus will spread further in the human population. A novel influenza H7N9 virus was first detected in humans in early 2013 and has since caused 250 human infections with 70 deaths. Similar incursions of avian influenza viruses into humans have probably taken place for as long as humans have had contact with poultry. We are now adept at detecting viruses and therefore we are noticing these infections more frequently.
Live poultry markets are clearly a risk factor for humans to acquire infections with avian influenza viruses, as noted by Perez and Garcia-Sastre:
Live bird markets in Asia are undoubtedly the major contributor in the evolution of avian influenza viruses with zoonotic potential, a fact for which we seem to remain oblivious.
Given their role in transmitting new viruses from animals to humans, I wonder why live poultry markets are not permanently closed.
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