Archive for the ‘Viruses’ Category

“New Virus Breaks The Rules Of Infection”! No – no, it doesn’t

31 August, 2016

I was prompted to this post by the breathless and much-hyped response to the discovery – the repeated discovery should I say; there was an earlier one that gets glossed over – of a multicomponent flavirus-like virus, this time in mosquitoes.

The actual report was published here: it is a well-done study, describing

“…a genetically distinct, segmented virus isolated from mosquitoes that also exhibits homology to viruses in the familyFlaviviridae and that appears to be multicomponent …, with each genome segment separately packaged into virions”

The authors say

“Although multicomponent genomes are relatively common among RNA viruses that infect plants and fungi, this method of genome organization has not previously been seen in animal viruses [my emphasis]

…which is why there’s all the hype, of course: claiming the virus “…breaks the rules of infection” is simply incorrect, because it is in fact related to very well characterised single-component ssRNA+ viruses of arthropods and mammals – flaviviruses – and infects its mosquito host exactly as these do, except with its genome in separate particles. Which makes it similar to quite a few plant viruses, several of which are, incidentally, probably evolutionarily related to viruses infecting insects – but more later.

Thus, a claim like “…a new study published Thursday is making researchers rethink how some viruses could infect animals” is simply hype.  But it is a sort of hype familiar to plant virologists, who after all showed that multicomponent viruses (=viruses with multipartite genomes packaged in separate particles) existed over 50 years ago – and who also showed that gene silencing was a factor in plant resistance to viruses long before their better-funded animal-researching colleagues got in on the act, but that is another story.

The way in which multicomponency was discovered with plant viruses is interesting: it relied on the fact that plants can respond with local lesions – qualitatively the same as plaques in bacterial or animal cell lawns – to mechanical infection, and that this can be used an an accurate assay of virus titre, as for phages or animal viruses (see here).  It became evident, though, that certain plant viruses produced significantly steeper lesion vs dilution curves than were expected from “one-hit” kinetics, where infection with a single virus particle sufficed to cause a lesion.

This is best shown by a plot like the one below, modified from REF Matthews’ Virology, 3rd Edn, attributed to Lous van Vloten-Doting from 1968.  This shows the curves obtained from accurate and painstaking local lesion assays with the single-component Tobacco necrosis virus (TNV), and the multicomponent Alfalfa mosaic virus (AMV): both are ssRNA+ and have isometric particles, but TNV has a single-component genome, and AMV a tripartite genome packaged in 3 particles.


The insect virus investigators did much the same thing:

“We used a similar approach to assay the nature of segment packaging for GCXV using cell culture plaques instead of leaf lesions. The dose-response curve for GCXV differed significantly from expectations for a single-component virus (i.e., the number of plaques decreased more quickly than expected with dilution of the inoculant)…we used our dose-response curve to estimate the presence of 3.27 ± 0.37 distinct GCXV particles required for plaque formation”

…but with the addition of rapid sequencing techniques not available in 1968, to show that indeed, the different segments were 5 distinct pieces of ssRNA, 3 mono- and 2 tricistronic (=3 ORFs), with the 2 largest monocistronic pieces being similar to flavivirus NSPs and the 3 smallest not encoding anything similar to sequences in the databases.  Four RNAs were essential for infectivity, while the smallest appeared dispensable.  Particles formed during infection of cultured cells were enveloped and 30-35 nm in diameter, considerably smaller than flavivirus virions.

This is a very interesting finding, although not unique: similar viruses were previously found in ticks in 2014, when the authors claimed that:

“To our knowledge, JMTV is the first example of a segmented RNA virus with a genome derived in part from unsegmented [flavi]viral ancestors

They were also wrong: there are a number of viruses for which this could have been said years ago, like the picornavirus superfamily-related comoviruses of plants. These have two-component genomes which both encode polyproteins, one with non-structural and the other with structural ORFs.  In fact, an evolutionary precursor to such viruses could be the more closely picornavirus-related dicistroviruses of insects, which have a classic picornavirus precursor polyprotein ORF split into two, with the structural protein ORF at the 3′ end and the regulatory or non-structural polyprotein at the 5′ end.

I got into this because it irked me mildly that such a fuss was being made of a second group of animal-infecting multicomponent ssRNA viruses, when the multicomponent plant virus precedent and history was VERY well established – but then got more interested when speculation started about what advantage multicomponency could confer on a virus.

I have thought for years that people discussing this generally have it backwards: it’s not that having a divided genome in separate particles offers advantage(s), it’s that it is not a DISadvantage in some circumstances – and particularly where there is no selection against the state.

A reason that multicomponency HAS been seen quite frequently with plant viruses could be that mechanically-transmitted viruses can reach VERY high concentrations in infected plants, and even obligately vector-transmitted viruses (eg: the bicomponent ssDNA begomoviruses, multicomponent ssDNA nanoviruses) reach quite high concentrations in the phloem tissue to and from which they are transmitted, compared to viruses in vertebrates.

This is also true for viruses of arthropods compared to vertebrate viruses: dicistroviruses in aphids can reach concentrations that are comparable to those of viruses like TMV in plants, to the point that aphids inject enough virus into plants that our lab originally mistook Rhopalosiphum padi virus for a plant virus. Moreover, plant virus virions often aggregate into quasi-crystalline arrays which can be hard to separate and which are even visible inside insect vectors, thus virtually guaranteeing that >1 virion will be present in any inoculum, even if significantly diluted.

This is most definitely NOT the case for vertebrate viruses, even where the same virus infects both an arthropod and a vertebrate host: the titre in the latter is guaranteed to be orders of magnitude lower, largely due to a more sophisticated immune system keeping viraemia in check. Thus, high inoculum concentrations relative to vertebrate viruses, and a tendency to aggregate, mean there is no DISadvantage inherent in multicomponency.

Having said this, there may be advantages to having a multicomponent genome: one such is presented in a recent article by Sicard et al. (2013), (thanks, @LauringLab and @DiagnosticChick!) in a study of the ssDNA nanovirus Faba bean necrotic stunt virus (FBNSV), which has an 8-component genome of ~1 kb/segment, encapsidated in 8 virions. They proposed:

“…that the differential control of gene/segment copy number may represent an unforeseen benefit for multipartite viruses, which may compensate for the extra costs induced by the low-frequency segments”

Thus, multicomponent viruses may achieve the sorts of gene dosage control only possible in viruses with larger genomes, by virtue of having multiple genome components rather than control elements which add genomic bulk.

Another possible advantage that I recall being touted by plant virological luminaries is the ease of reassortment compared to recombination: this is exemplified by the reo- and orthomyxoviruses, albeit in vertebrates, where they are constrained by having to have all genome components in the same capsid to guarantee infectivity.

I think Vincent Racaniello is correct in the breathless article I quoted in opening, where he is quoted as saying

“There’s so much we don’t know about viruses…We should always expect the unexpected.”

Absolutely. And I think it’s a safe bet that a LOT more multicomponent viruses will be found in arthropods – and even in some vertebrates, to which they will have been transmitted by arthropods. Because that’s the link between many of these viruses: an evolutionary history that involves plants and arthropods, or arthropods and other animals, at an early stage of life on land. Because that’s all there was for advanced eukaryotes, early on: primitive vascular plants, insects that preyed on them and on each other, and protists.

Bunyaviruses in protozoa?

25 August, 2016

A Novel Bunyavirus-Like Virus of Trypanosomatid Protist Parasites

  1. Natalia S. Akopyantsa,
  2. Lon-Fye Lyea,
  3. Deborah E. Dobsona,
  4. Julius Lukešb,c,
  5. Stephen M. Beverleya


We report here the sequences for all three segments of a novel RNA virus (LepmorLBV1) from the insect trypanosomatid parasite Leptomonas moramango. This virus belongs to a newly discovered group of bunyavirus-like elements termed Leishbunyaviruses (LBV), the first discovered from protists related to arboviruses infecting humans.


OK, seriously interesting viruses – BECAUSE “…The L. moramango virus thus resembles a group of related viruses discovered recently in the closely related human parasite Leishmania”…which I will note, whose phylogenetic affinity to other higher eukaryotes is via a relationship to trypanonosomes, and then – Euglena??  Which is an alga….

Seriously: a bunya-like virus found in a protozoan whose closest affinity to other hosts of bunyaviruses is via algae??
This pushes the possible evolutionary origin of bunyaviruses faaaaaar back, to possibly a billion years or so, when fungi were separating from protists from algae…..
There is another option, however: I note the Leptomonas sp. is a parasite of insects. It is of course worth noting that the Leishmania and other related parasites infecting mammals are also all arthropod-vectored – which could imply an origin in arthropods.
Which makes good sense, considering these beasties date back less than 600 million years or so – which is still pretty good for a virus?!

So: will smallpox come back to kill us, from the melting permafrost??

17 August, 2016
Variola virus, the agent of smallpox.  Image courtesy Russell Kightley Media.

Variola virus, the agent of smallpox. Image courtesy Russell Kightley Media.

There has been a lot of tweeting today about how Smallpox Will Come Back From The Grave And Kill Us All: see here, here and here for lurid examples.

This is alarmism at its insidious best: shouting out a headline, based on flimsy evidence, that says “We’re all going to die!” or similar nonsense.

Really: this IS nonsense.  Some corpses were found in the permafrost in Siberia, that MAY have had smallpox-like lesions on them, and from some of which which smallpox virus DNA could be recovered – presumably by PCR.

This does NOT constitute a threat of live virus being present, or escaping from the corpses even if it WERE there.  I have railed on about this sort of thing before, and I am as unconvinced now as I was then, albeit with SOME reservation about the possibility for smallpox.

"Pithovirus sibericum", from Jean-Michel Claverie and Chantal Abergel

“Pithovirus sibericum”, from Jean-Michel Claverie and Chantal Abergel

I can believe you could get live anthrax: those spores are incredibly tough, and can last for many years in soil, let alone in ice. I could also believe that one could find live megaviruses – the so-called pitho- and molliviruses – in permafrost, because their putative hosts are unicellular protozoans and because they are also seriously stable.

But smallpox? The virus is probably not as stable as the megaviruses mentioned; it relies for infection on its structure, which has membranes integral to it – AND it infects people, who, when they die, don’t cool down very quickly, and whose cells release all sorts of nasty enzymes (lipases, proteases) as they die. Which could be expected to chew up most things, including poxviruses.

Oh, sure, poxviruses CAN survive for years at a pinch – in the form of dried secretions or scabs, which, because they are dehydrated and full of protein, tend to stabilise virus particles. This is how the old variolators and vaccinators (literally: people who used variola or “vaccine” to vaccinate against smallpox) used to preserve their inocula, when they weren’t using fresh material.

Melting tundra is not like that, I will note: bodies with intact virions in them will thaw and rot all over again, and that rotting will reduce what little virus there may be even further.

So I am not a believer in Death From The Permafrost!

And nor should you be.  But it might not hurt for someone qualified to test whether or not there IS live virus in frozen samples, by culturing an extract?

The Internet Journal of Comprehensive Virology

15 July, 2016


See Home Page for details

New developments in a South African HIV vaccine trial

7 June, 2016
HIV life cycle - Russell Kightley Media

HIV life cycle – Russell Kightley Media

Subtype C gp140 Vaccine Boosts Immune Responses Primed by the South African AIDS Vaccine Initiative DNA-C2 and MVA-C HIV Vaccines after More than a 2-Year Gap 

A phase I safety and immunogenicity study investigated South African AIDS Vaccine Initiative (SAAVI) HIV-1 subtype C (HIV-1C) DNA vaccine encoding Gag-RT-Tat-Nef and gp150, boosted with modified vaccinia Ankara (MVA) expressing matched antigens. Following the finding of partial protective efficacy in the RV144 HIV vaccine efficacy trial, a protein boost with HIV-1 subtype C V2-deleted gp140 with MF59 was added to the regimen. A total of 48 participants (12 U.S. participants and 36 Republic of South Africa [RSA] participants) were randomized to receive 3 intramuscular (i.m.) doses of SAAVI DNA-C2 of 4 mg (months 0, 1, and 2) and 2 i.m. doses of SAAVI MVA-C of 1.45 × 109 PFU (months 4 and 5) (n = 40) or of a placebo (n = 8). Approximately 2 years after vaccination, 27 participants were rerandomized to receive gp140/MF59 at 100 μg or placebo, as 2 i.m. injections, 3 months apart. The vaccine regimen was safe and well tolerated. After the DNA-MVA regimen, CD4+ T-cell and CD8+ T-cell responses occurred in 74% and 32% of the participants, respectively. The protein boost increased CD4+ T-cell responses to 87% of the subjects. All participants developed tier 1 HIV-1C neutralizing antibody responses as well as durable Env binding antibodies that recognized linear V3 and C5 peptides. The HIV-1 subtype C DNA-MVA vaccine regimen showed promising cellular immunogenicity. Boosting with gp140/MF59 enhanced levels of binding and neutralizing antibodies as well as CD4+ T-cell responses to HIV-1 envelope. (This study has been registered at under registration no. NCT00574600 and NCT01423825.)

This is a pretty big deal – because it reports an extension of a wholly South African-originated vaccine trial, that consisted of a DNA prime with a subtype C gp150 gene and an artificial Gag-RT-Tat-Nef polyprotein gene, followed by a rMVA boost, that was as immunogenic as anything else trialled around the same time.

And development of which was shut down for political reasons in 2009, but that is old news….
This new development, where a subtype C gp140 (soluble form of Env) was given with MF59 adjuvant to trial participants 2 years after the initial vaccinations, showed that recall responses were strong – in both cellular and humoral arms of the immune system. Moreover, neutralising Ab were elicited.
This is a very promising development in the saga of HIV vaccinology, and it is to be hoped that further trials will be funded.
And both my sister-in-law and my wife are involved B-) What can I say, we’re a virological family!

AIDS: 35 years old this month

6 June, 2016
HIV particle.  Russell Kightley Media

HIV particle. Russell Kightley Media

I was alerted via Twitter this morning to the fact that the CDC’s Morbidity and Mortality Weekly report that reported the first recognition of the syndrome we now know as AIDS, was published on 5th of June 1981.  It appears – sadly – that their archive only goes back to 1982: there’s a missed chance to expose some history, CDC?!

Thirty five years: I was a novice lecturer, just starting out; the Web was still science fiction; HIV and its relatives were still undiscovered – but they had already started to spread out of Africa, after smouldering away in the tropical forests of Gabon and the Congos for decades.

I started an information web page on HIV/AIDS back in 2000 or so, largely in response to the ridiculousness of Thabo Mbeki’s pronouncements on the virus and the disease: thanks to tectonic shifts in the UCT Web policy, these disappeared – but thanks to the invaluable Wayback Machine, can still be found.  If you want a slice of history, and to see how bad I am at designing web pages, go take a look. Still MOSTLY valid, although many of the links are now dead – sic transit the web content, unfortunately!

And here we are in 2016: I’m now an elderly academic, the Honours student who alerted me to the fact the the “GRIDS” syndrome virus may have been identified in 1983 is now a senior Professor and distinguished HIV researcher – there’s a whole career there, Carolyn! – and HIV/AIDS is still with us. And unfortunately, Thabo Mbeki is still being wilfully if not malevolently ignorant, and I am still feeling it necessary to crap on him.

At least the pandemic appears to have peaked in terms of incidence, and ARVs are increasingly good and employed widely; however, we still don’t have a decent vaccine, and people are still being infected. This pandemic will last out my career – but hopefully not those of some of the people I have trained.

“Online ‘recipes’ for bird flu virus add to bioterrorism threat!” No. No, they don’t.

10 December, 2015

The means of engineering potentially deadly avian influenza is freely available on the internet.

Despite continuing global efforts to contain avian influenza, or bird flu, the means of engineering this potentially deadly H5N1 virus to render it transmissible to humans is freely available on the internet. So too are similar instructions for engineering a virus like the “Spanish flu”, which killed some 50 million people in the pandemic of 1918-19.

The digital floodgates opened in 2011 when a peak US regulatory watchdog came down in favour of scientists seeking to publishing their work engineering the H5N1 virus. The decision to uphold such “scientific freedom” was and remains, highly contentious among the global scientific community. Its implications, however, are readily available as online “recipes” for potentially dangerous viruses, which add a new risk to the already considerable challenges of maintaining global biosecurity in the 21st century. For all the recent advances in biomedical science, drugs, vaccines and technology, this is a challenge we remain ill-equipped to meet.

Follow us: @theage on Twitter | theageAustralia on Facebook

Sourced through from:


OFFS: seriously!  Again?!  Someone else has just discovered that entire virus genomes are freely available via PubMed, along with papers on gain-of-function experiments, and immediately leaps to the conclusion that this means “…the means of engineering this potentially deadly H5N1 virus to render it transmissible to humans is freely available on the internet”.

I’m sorry, this is being simple-minded to the point of parody.  I have written elsewhere – here in ViroBlogy, and in Nature Biotech’s Bioentrepreneur blog section – on how it is MOST unlikely that bearded fellows in caves in Afghanistan or remote farms in Montana are going to whip up weaponised batches of H5N1 flu or Ebola.

Yes, the papers are available; yes, the sequences necessary to make a potentially (and I say potentially advisedly) deadly virus are available online; yes, one can bypass the blocks on getting resynthesised genes in developing countries (hint: China).

But could anyone outside of a sophisticated lab environment use these to make anything nasty?


Seriously, no.

Just think about what you would need to make weaponised flu, for example.  There are two ways to go here, these being the totally synthetic route (“mail order” DNA – HATE that term!), with some serious molecular biology and cell culture at the end of it, and the “natural” route – which would involve getting a natural and nasty isolate of H5N1 / H7N9 / H9N2, and being able to culture it and engineer it as well.

Both routes require a minimum of a serious 4-yr-degree-level training in microbiology / mol biol, as well as laboratory resources that would include incubators, biohazard cabinets, and disposables and reagents that are not on your normal terrorist’s priority purchase list.

In fact, the kinds of resources you’d find at a University or Institute Infectious Disease unit – or state-sponsored biowarfare lab.

Seriously, now: in order to use the information that is “freely available”, you’d have to do what amounts to an entire postgrad degree’s worth of work just to set up the kinds of reverse genetics necessary to WORK with recombinant flu, presuming you already had an isolate, and even more than that if you were to start with synthesised DNA and try to recreate infectious virus.

Again, this is the kind of work they do in biowarfare / biodefence labs (funny how they’re pretty much the same thing, isn’t it?) – because it’s finicky, expensive, laborious – and potentially dangerous to the researcher.

And it’s interesting that the only rumoured escapes of biowarfare agents have been of flu in 1977 in the old Soviet Union, and of anthrax in Sverdlovsk in the USSR in 1979. And in the US in 2001, and again in 2014.  ALL of them from official facilities, I will discreetly point out.

Oh, there have been rumours that Saddam’s Iraq weaponised camelpox; that the USSR/Russia cloned Ebola into a poxvirus; that Al-Qaeda tested anthrax – but the first two took state resources, and if the third happened at all, it’s nothing that the UK and USA and friends hadn’t already done in the 1940s.



See on Scoop.itVirology News

Testing out a textbook on Virology

5 December, 2015

Like my recent books on History of Viruses and Influenza, I’m constructing an ebook Introduction to Virology textbook – and I’d like people’s opinions.

It’s going to look something like this:



It will be based on my web pages that were so cruelly destroyed, but will be PROFUSELY illustrated, using all of the bells and whistles built into the iBooks Author app, with liberal use of Russell Kightley’s very excellent virus picture library.

And I will sell it for US$20 or less.

Tell me what you think of the taster – and there will be more.

Rounding Up The Last Of A Deadly Cattle Virus

16 November, 2015

Rinderpest, or cattle plague, was declared eradicated in 2011. But many research institutes still have samples of the rinderpest virus in storage. Disease experts want those samples destroyed.

Sourced through from:

I have written a lot about rinderpest, and covered it in my book on virus history, as well as covering the debate on whether or not smallpox virus stocks should be eliminated.

And if they haven’t yet, despite years of debate, why should rinderpest virus stocks?

Consider: we have an effective vaccine(s); we still have the related peste des petits ruminants virus knocking around, with vaccines to it – so why shouldn’t stocks of the live virus strains be preserved?

How many viruses have in fact made it out of fridges, and back into the world?  Well, there was that purported 1977 H1N1 release in Russia/Mongolia…but can anyone think of another well-documented one?  Just one?

The fact is that it is FAR easier to deliberately spread endemic viruses around – like foot-and-mouth disease virus – than it would be to reactivate and spread something from a lab freezer.

Rather let us conduct an inventory of who has what, consolidate it like they did with smallpox, and forget about the unknowable, which is obscure freezers in far-flung rural centres where no-one remembers what is there – and where powercuts have probably thawed the samples more than once.

See on Scoop.itVirology News

So that’s what you lot like, is it?

21 October, 2015