Archive for August, 2012

Medicago Announces 2012 Second Quarter Financial Results: PR Newswire

15 August, 2012

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Medicago Announces 2012 Second Quarter Financial Results PR Newswire QUEBEC CITY, Aug. 14, 2012 QUEBEC CITY , Aug. 14, 2012 /PRNewswire/ – Medicago Inc.

“Subsequent to the second quarter:

Announced the successful completion of a key milestone under an agreement with the Defense Advanced Research Projects Agency (DARPA). The milestone was the production of at least 10 million doses of H1N1 VLP influenza vaccine candidate in one month (the “rapid fire test”). The rapid fire test was conducted at Medicago’s facility in Durham, North Carolina. As part of the rapid fire test, production of the H1N1 VLP influenza vaccine candidate began on March 25th, 2012, and was completed in 30 days on April 24th, 2012. The production lots were then tested by a third party laboratory to confirm both the immunogenicity of the vaccine candidate and the number of doses produced. Testing confirmed that a single dose of the H1N1 VLP influenza vaccine candidate induced protective levels of neutralizing antibodies in an animal model. The production of significantly more than 10 million doses, as defined by the testing conditions, were confirmed.”

This is a big, big deal – because they did this via transient epxression in plants, thus proving pretty much beyond doubt that this is now a serious vaccine manufacturing technology.

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Hepatitis A Vaccine for Children Lasts for 10 Years

15 August, 2012

See on Scoop.itVirology News

“Children younger than 2 who are given the hepatitis A vaccine are protected from the virus for 10 years, a new study shows.

Hepatitis A is a virus that causes inflammation of the liver, and typically is found in areas with poor sanitation where it is transmitted through contaminated food and water.

Researchers from the U.S. Centers for Disease Control and Prevention found that the transfer of a mother’s hepatitis A antibodies — which help defend against the virus — to her child does not reduce the effectiveness of the vaccine, which is routinely given to children between 12 months and 18 months old.”


Good news indeed – because the vaccine hasn’t been around that long, and it’s always useful to know just when you might need re-jabbing.  A seriously good idea for people travelling in Africa, Asia, South America….

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Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes

15 August, 2012

See on Scoop.itVirology and Bioinformatics from

The Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) constitute an apparently monophyletic group that consists of at least 6 families of viruses infecting a broad variety of eukaryotic hosts. A comprehensive genome comparison and maximum-likelihood reconstruction of the NCLDV evolution revealed a set of approximately 50 conserved, core genes that could be mapped to the genome of the common ancestor of this class of eukaryotic viruses.

We performed a detailed phylogenetic analysis of these core NCLDV genes and applied the constrained tree approach to show that the majority of the core genes are unlikely to be monophyletic. Several of the core genes have been independently acquired from different sources by different NCLDV lineages whereas for the majority of these genes displacement by homologs from cellular organisms in one or more groups of the NCLDV was demonstrated.

A detailed study of the evolution of the genomic core of the NCLDV reveals substantial complexity and diversity of evolutionary scenarios that was largely unsuspected previously. The phylogenetic coherence between the core genes is sufficient to validate the hypothesis on the evolution of all NCLDV from a common ancestral virus although the set of ancestral genes might be smaller than previously inferred from patterns of gene presence-absence.


Interesting stuff!  Strengthens my contention that  “…a virus is an infectious acellular entity composed of compatible genomic components derived from a pool of genetic elements” –

Baculovirus image from my collection

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Adaptive Changes in Alphavirus mRNA Translation Allowed Colonization of Vertebrate Hosts

10 August, 2012

See on Scoop.itVirology and Bioinformatics from

“Genetic, phylogenetic, and biochemical data presented here support an evolutionary scenario for the natural history of alphaviruses, in which the acquisition of DLP structure in their mRNAs probably allowed the colonization of vertebrate host and the consequent geographic expansion of some of these viruses worldwide.”


I have taught for some time now that the evolution of many mammalian viruses must have involved adaptation of originally (and sometimes still) insect-infecting agents – given that insects crawled out onto dry land quite a long time before vertebrates did.  This is a nice illustration of that.  Pity I don’t teach anymore B-(

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Schmallenberg virus: A new Shamonda/Sathuperi-like virus on the rise in Europe

9 August, 2012

See on Scoop.itVirology News

“In the summer-fall of 2011, a nonspecific febrile syndrome characterized by hyperthermia, drop in milk production and watery diarrhea was reported in adult dairy cows from a series of farms located in North-West Europe. Further, in November 2011, an enzootic outbreak of abortion, stillbirth and birth at term of lambs, kids and calves with neurologic signs and/or head, spine or limb malformations emerged throughout several European countries. Both syndromes were associated with the presence in the blood (adults) or in the central nervous system (newborns) of the genome of a new Shamonda-Sathuperi reassortant orthobunyavirus provisionally named Schmallenberg virus after the place where the first positive samples were collected. The clinical, pathological, virological and epidemiological facts that were made publicly available during the first 6 months after the emergence are presented here. Current knowledge of the epidemiology of the phylogenetically closest relatives of the newcomer (Shamonda, Sathuperi, Aino and Akabane viruses) is not exhaustive enough to predict whether the current outbreak of Schmallenberg virus is the prelude to endemicity or to a 2 years long outbreak before the infection burns out when serologically naïve animals are no longer available. In the future, cyclic epizootic reemergences are a possibility too, either synchronized with a global decrease of herd immunity or due to antigenic variants escaping the immunity acquired against their predecessors. The latter hypothesis seems unlikely because of the wide array of biologic constraints acting on the genome of viruses whose life cycle requires transmission by a vector, which represses genetic drift. The remarkable stability of the Shamonda virus genome over the last forty years is reassuring in this regard.”

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Evaluation of methods to concentrate and p… [Environ Microbiol. 2012] – PubMed – NCBI

9 August, 2012

See on Scoop.itAquatic Viruses

“Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration and purification methods across four combinations as follows: (i) tangential flow filtration (TFF) and DNase + CsCl, (ii) FeCl(3) precipitation and DNase, (iii) FeCl(3) precipitation and DNase + CsCl and (iv) FeCl(3) precipitation and DNase + sucrose. Taxonomic data (30% of reads) suggested that purification methods were statistically indistinguishable at any taxonomic level while concentration methods were significantly different at family and genus levels. Specifically, TFF-concentrated viral metagenomes had significantly fewer abundant viral types (Podoviridae and Phycodnaviridae) and more variability among Myoviridae than FeCl(3) -precipitated viral metagenomes. More comprehensive analyses using protein clusters (66% of reads) and k-mers (100% of reads) showed 50-53% of these data were common to all four methods, and revealed trace bacterial DNA contamination in TFF-concentrated metagenomes and one of three replicates concentrated using FeCl(3) and purified by DNase alone. Shared k-mer analyses also revealed that polymerases used in amplification impact the resulting metagenomes, with TaKaRa enriching for ‘rare’ reads relative to PfuTurbo. Together these results provide empirical data for making experimental design decisions in culture-independent viral ecology studies.”


Things just keep getting easier and easier…now to do some work!

Mimivirus graphic courtesy of Russell Kightely Media

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Ebola Outbreak in Uganda: CDC Rushes to Contain Virus

8 August, 2012

See on Scoop.itVirology News

Dr. Richard Besser travels with American doctors as they race to stop a global threat.


Really? Because local doctors were doing nothing about it? Because it was really a global threat? Come on! The Kikwit outbreak in the 1990s was MUCH worse, occurred in a much more chaotic public health setting – and less than 0.1% of the city of 500 000 was affected, and it didn’t spread.
Be more afraid of…oh, I don’t know, maybe West Nile virus, Dengue virus, Yellow fever virus?? WAAY more cases, and far closer to the US of A!

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Setting your virus free

7 August, 2012

I was reminded, as I walked in my garden in the Cape Town late afternoon sun a short while ago, of a Master’s degree project I had started with a very bright young person.  A young person who didn’t finish, because she abandoned her degree in the interests of finding herself – and subsequently got into computer-based education some 16 years ago, but that’s another story.

I have written about her previously, as it happens: she is the “Dr” Jacobson in this story, written about a year after her Honours essay on Emerging Viruses became the most authoritative source in the world on Ebola virus that was available electronically – and the Kikwit Ebola outbreak that occurred soon afterwards caused the world to go frantically looking for information.

Sadly for her, she could not work on Ebola for her Master’s, so I gave her what I thought was the next best thing: a project on making a replicating DNA vector system out of Abutilon mosaic virus (AbMV), a two-component ssDNA begomovirus.  The project started in the easiest way imaginable: she went to the local plant nursery, and bought a variegated Abutilon striatum in a pot, and planted it in our Departmental plant room.

Abutilon leaves and flower

AbMV in what is now an ornamental abutilon produces very striking symptoms, which accounts for the popularity of the plant, and its spread across much of the world – by cuttings, mainly.  This is fortunate, as in most cases the virus has lost its natural mode of transmission, which is only via whiteflies (Bemisia tabaci).  Thus, by fortuitous accident, a virus that is  effectively crippled is now spread far beyond its point of origin in South America, purely by human intervention.

Be this as it may, our mission was to harness the fact that AbMV maintains itself as an episome for the lifetime of a plant by making it into an expression vector for plant-made vaccines.  Kenneth Palmer in my lab had already done similar work with Maize streak virus; however, maize was not really a usable host because it is an annual and was hard to infect and the vector did not spread.  It was also not usable in dicot hosts, so we settled on AbMV as being available in our and many other back yards.

We did not get far: while Alison was really bright, by this time she had discovered that science really wasn’t for her, and made essentially no progress beyond cloning a B genome and getting some sequence out of it.  She left to find more fulfilling things to do, and her experimental material continued to grow in the plant room – and gather red spider mites.  I still have the badge off her labcoat, incidentally: I couldn’t let it go; it was and is the only Led Zeppelin logo I have ever seen on the standard white coat.

This is where we get to the title of this post. In 1996 or so, I took the by-now largish plant in its pot back home, and set it free: I planted it in my garden.  It eventually developed into a large bush, easily 3 x 2 metres wide and tall – and has just been cut back, after some 16 years, to allow it to redevelop.  I get a little kick out of seeing civilians step nervously away from it, after I have walked them up to it, and say: “And this is the biggest virus you will ever meet”.  Let’s see you do THAT, Ebola virologists!

Oh, it isn’t entirely free: we sampled it again a couple of years ago when the fearsomely efficient geminivirus-hunting crew that grew out of my lab wanted samples to test their then-new phi29 rolling circle amplification chops on.  We could still only get a B genome out of it, and one that was 10% different from any other published AbMV – so maybe there’s still a story there.

But all it has to do now is keep on growing.  And look beautiful.

Viruses linked to prostate cancer – ABC News (Australian Broadcasting Corporation)

1 August, 2012

See on Scoop.itVirology News

Australian scientists have made an important discovery about prostate cancer.

Nice little video: of course, they don’t say WHICH papillomaviruses are involved, along with Epstein-Barr virus.  Anyway – as long as it’s 16 and 18, good reason to get vaccinated, boys!  I thank Russell Kightley for sending me the clip.

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More Ugandans Admitted with Possible Ebola

1 August, 2012

See on Scoop.itVirology News

Date: Tue 31 Jul 2012
Source: Time Healthland, Associated Press report [edited]

More Ugandans Admitted with Possible Ebola
A total of 6 more patients suspected to have Ebola have been admitted to the hospital days after investigators confirmed an outbreak of the highly infectious disease in a remote corner of western Uganda, a health official said on Monday [30 Jul 2012]. Stephen Byaruhanga, health secretary of the affected Kibaale district, said possible cases of Ebola, at 1st concentrated in a single village, are now being reported in more villages. “It’s no longer just one village. There are many villages affected,” Byaruhanga said. In a national address on Monday, Uganda’s President advised against unnecessary contact among people, saying suspected cases of Ebola should be reported immediately to health officials.

Officials from Uganda’s Ministry of Health and the World Health Organization announced on Saturday [28 Jul 2012] that the deadly Ebola virus killed 14 Ugandans this month, ending weeks of speculation about the cause of a strange illness that had some people fleeing their homes in the absence of reliable answers. If the 6 new cases are confirmed as Ebola fever, it would bring to 26 the number of Ugandans infected with Ebola [virus].

This is the 4th occurrence of Ebola in Uganda since 2000, when the disease killed 224 people and left hundreds more traumatized in norther Uganda. At least 42 people were killed in another outbreak in 2007, and there was a lone Ebola case in 2011. Investigators took nearly a month to confirm Ebola’s presence in Uganda this year. In Kibaale, a district with 600 000 residents, some villagers started abandoning their homes to escape what they thought was an illness caused by bad luck. One family lost 9 members, and a clinical officer and her 4-month-old baby died from Ebola, Byaruhanga said.

D.K. Lwamafa, of Uganda’s Ministry of Health, told reporters on Saturday that one Ebola patient from Kibaale had been referred to the national hospital in the capital but had then died in Kibaale.

The confirmation of Ebola’s presence in the area has spread anxiety among sick villagers, who are refusing to go the hospital for fear they don’t have Ebola and will contract it there. All suspected Ebola patients have been isolated at one hospital where patients admitted with other illnesses fled after Ebola was announced. Only the hospital’s maternity ward still has patients, officials said, highlighting the deadly reputation of Ebola in a country where the authorities do not always respond quickly and effectively to emergencies and disasters. Barnabas Tinkasimire, a lawmaker from the area, said that some nurses refused to look after Ebola patients after one clinical officer died and another was taken ill.

“They are saying, ‘We can’t remain here if there is no sufficient allowance’,” Tinkasimire said of medical officers handling Ebola cases. The lawmaker said the government’s response so far has been poor and that it would have been worse without the technical support of organizations such as the World Health Organization and the U.S. Centers for Disease Control and Prevention (CDC). “It took long for the government to respond, and up to now many people don’t know how to guard against Ebola. We need sensitization,” he said.

Ebola, which manifests itself as a hemorrhagic fever [But not in this outbreak – Mod.CP], is highly infectious and kills quickly. It was 1st reported in 1976 in Congo and is named for the river where it was recognized. A CDC factsheet on Ebola says the disease is “characterized by fever, headache, joint and muscle aches, sore throat, and weakness, followed by diarrhea, vomiting, and stomach pain. A rash, red eyes, hiccups and internal and external bleeding may be seen in some patients.”

Scientists don’t know the natural reservoir of the virus, but they suspect the 1st victim in an Ebola outbreak gets infected through contact with an infected animal. The virus can be transmitted through direct contact with the blood or secretions of an infected person, or objects that have been contaminated with infected secretions. During communal funerals, for example, when the bereaved come into contact with an Ebola victim, the virus can be contracted, health officials said.

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ProMED-mail from HealthMap alerts

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