Archive for the ‘GMOs’ Category

From plant virology to vaccinology: a personal journey

15 February, 2017

A couple of years ago now, an Editor of the journal Human Vaccines & Immunotherapeutics contacted me to say they would like to profile me as a vaccinologist. Being of a suspicious nature, I immediately inquired how much this would cost me. The encouraging answer was “Nothing!” – so I jumped straight in.

The end result is as near to a current autobiography as I will probably ever get, so I may as well put it up here. So, if you’re interested in finding out what the connections are between a swimming pool in Zambia, not doing Biochemistry (twice), plant virology and making vaccines – click below!

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!

New Approaches to Vaccines for Human and Veterinary Tropical Diseases. Or maybe sophisticated safari science?

27 May, 2016

The Keystone Symposia organisation held a meeting entitled “New Approaches to Vaccines for Human and Veterinary Tropical Diseases” in Cape Town this week (May 22-26, 2016).  A summary of the meeting was given as:

Human and livestock vaccines can contribute to improved human welfare and income generation by maintaining human health and meeting the demand for meat, milk and fish in developing countries. All of these factors contribute to the growing importance of improving food safety, availability and nutritional security. An important component of this Keystone Symposia meeting will be to stimulate crosstalk between the human and veterinary vaccine communities by highlighting cross-cutting technical advances and new science and knowledge from laboratory and field research. The meeting will also provide a rare opportunity for scientists from the Northern and Southern hemispheres to interact and pool resources and knowledge in the common fight against tropical diseases.”

It succeeded admirably in a couple of these goals: there were delegates there from 31 African countries, as well as many Europeans, Brits and Americans; the juxtaposition of veterinary and medical talks on similar themes created an excited buzz among folk who hadn’t been exposed to the “other”; there was a wealth of dazzling new tech on display in talks, and intriguing insights into how similar – and sometimes, how different – human and animal responses to vaccines were.  It was obvious that approaches used to develop malaria vaccines could benefit animal vaccinology, and indeed, Vish Nene and colleagues from ILRI in Kenya are following some of the same approaches in their work with the East Coast fever disease organism in cattle.

But, there were a couple of buts.  An important one for me was that while there were many Africans there, they were not much exposed in talks, apart from several South Africans. While amazing results were displayed from deep sequencing of antibody gene repertoires of humans and animals and how these developed with affinity maturation; while grand predictions were made as to how bioinformatics and molecular design would revolutionise vaccinology – this was more of the same kind of thing we have got used to in HIV vaccine meetings over nearly twenty years, where Big Science is always going to provide a solution, but never quite gets to it. Why was there no mention of ZMapp antibody therapy for Ebola, when this (OK, I’m biased) was the single most exciting thing to come out of the Ebola outbreak and the international response to it?

I hate to be cynical, but seriously: is there one single vaccine in advanced human trial right now that is a result of intelligent molecular design? Has ANYTHING that has been designed from crystallographic evidence or from cryoEM data actually proven useful in animals or people?  Has dissection of the anti-HIV antibody response development actually, really, taught us anything useful about how we should develop vaccines? Even if South Africans were involved?

I told you I was cynical – and my cynicism was reinforced by a couple of displays of “My Ebola vaccine is better than YOUR Ebola vaccine!”, by folk who shall remain nameless – when it was obvious that both ChAdOx and rVSV vaccines have their merits.

Mind you, the tale of how Ebola vaccines were deployed so rapidly, and how what could have been a 15+ year saga was compressed to less than a year for the rVSV-ZEBOV and ChAdOx vaccines was truly inspirational. It is indeed an object lesson in how to respond to an emerging disease that big companies and philanthropic organisations were able to make many thousand doses of different vaccine candidates in just a few months, and that these could be deployed in human “trials” – actually, genuine deployment in ring vaccination for the VSV candidate – almost immediately.  Adrian Hill of Oxford asked the question, albeit outside the meeting at a seminar in our Institute: if this was possible for an Ebola outbreak, why isn’t it possible for everything else?  Why can’t we do it for Zika virus, and for MERS-CoV too?

If there is a Big Lesson to come out of this meeting, why can’t it be – Let’s Make Vaccines Faster!

Oh, there were big plusses too.  There were fascinating parallels to be drawn in the approaches to developing vaccines for malaria and TB and animal parasitic infections; some of the fancier techniques discussed for human vaccines could obviously find applications in veterinary vaccinology; there were even suggestions for vaccine candidates for animals that were drawn from homologous genes in human and animal apicomplexans (=malaria-like organisms).

I was especially impressed by Dean Everett‘s talk, from the Malawi-Liverpool-Wellcome Trust Clinical Research Programme in Malawi, on “Developing Appropriate Vaccines through Bioinformatics in Africa”: they were actually working in under-developed Africa, on pressing local problems, and making significant inroads into the problems.

And yet, and yet: I have railed elsewhere about the J Craig Venter Institute’s grandstanding over their “synthetic” organisms; while the talk here by Sanjay Vashee on “Synthetic Bacterial and Viral Backbones as Antigen Delivery Vehicle” went some way to redeeming my negative impression of the use of this sort of work, I am still left with the impression that there are considerably easier ways of doing what they claim to be able to. Mind you, one of my colleagues was very impressed with the possibility of making Herpesmids (=infectious, engineerable whole genome clones) in yeast, and would love to do it with their poxvirus collection – so maybe I am a touch TOO too cynical.

I also felt that the final address, by Chris Wilson of the Bill & Melinda Gates Foundation, on: “Cross-Disciplinary Science to Accelerate the Discovery of Vaccines for Global, Zoonotic and Emerging Infectious Diseases” exemplified some of the problems inherent in trying to marry up developed and developing world science, especially in vaccinology.  Part of the talk was great: he gave the best description I’ve yet heard of why it could be feasible to inoculate Aedes spp. with Wolbachia, and why it could significantly impact transmission of flavi- and other viruses.  His description of gene drive technology for wiping out selected mosquito populations was also succinct, and masterly – and appropriate for a developing world audience. Then he got on to how dissection of antibody maturation pathways and flavivirus E protein design could provide paths to good vaccines, and the cynicism kicked in again.

We don’t need either technology to get to vaccines for HIV or for flaviviruses that we can test in the near future, and which could have very significant impacts on millions of people.

Really: we don’t. Extant HIV vaccine candidates are almost certainly better than the RV144 Thai trial vaccine components, and they had an efficacy of 60% in the first year. We already have YFV and dengue and JEV live vaccines – why don’t we use one or several of them in combination with an engineered YFV vaccine to protect against ALL epidemic flaviviruses?  Given the Ebola example, we could deploy vaccines for HIV and for flaviviruses in a year or less, and they would have an impact that would tide us over while fancier products were being made. Seriously: we are always waiting for the next best thing; let’s just apply what we know and what we have NOW to make an impact – instead of, like theoretical physicists, perpetually considering the problem of the spherical horse instead of just going out and riding one.

And that should have been one of the Big Lessons, and we missed it. Instead, there was an element of Safari Science, which is what we in Africa call the kind of endeavour which involves people from the global North flying in to sort out our problems – and leaving with our organisms and disease samples.

Which we could do ourselves, given funding. And that’s another lesson for the folk that do Big Science funding….


Your next DNA vaccine might come from tobacco

12 February, 2016

We don’t have much practice at this sort of thing, but seeing as we just got something REALLY cool published, and the man who largely made it possible is now a science writer, we decided to ask him to write a press release.  So he did.  Thanks, Paul Kennedy – take a bow, twice!

“In a pioneering step towards using plants to produce vaccines against cervical cancer and other viruses, University of Cape Town (UCT) researchers have generated synthetic human papillomavirus- derived viral particles called pseudovirions in tobacco plants.

“We’ve succeeded in making a completely mammalian viral particle in a plant – proteins, DNA, everything. That’s enormously exciting,” says Dr Inga Hitzeroth of the Biopharming Research Unit (BRU) at UCT.Dr_Inga_Hitzeroth

In an Open Access study just published in Nature Scientific Reports, BRU researchers report using tobacco plants to create a synthetic viral particle known as a pseudovirion.

A pseudovirion looks like a virus, but it contains no infectious viral DNA. A virus is usually made up of a shell surrounding the virus’s own genetic material. Pseudovirions instead carry whatever DNA the researcher wishes to include within the shell of proteins that make up the outer coating of the virus.

Until now, such particles have only ever been created in yeast or mammalian cell cultures – this is the first time researchers have successfully created pseudovirions in plants.

The BRU is part of a new movement known as biopharming, which means using plants as biological factories. Biopharming has been used to create flu vaccines, potential Ebola drugs, and an enzyme used to treat Gaucher’s Disease in humans. The technique employs the cellular machinery within tobacco plants or other plant cells to manufacture enzymes, antibodies or even the viral capsid proteins (the proteins that make up the shell of a virus), which act as vaccines.

In this research, the BRU has taken biopharming one step further by using plants to create a viral shell that encloses ‘custom’ DNA selected by researchers. “What’s unique here is that DNA that was manufactured within the tobacco plant is now being incorporated into a viral particle to form a pseudovirion,” says Hitzeroth.

The shell of this pseudovirion was that of human papillomavirus (HPV) type 16, the virus responsible for over 50% of cervical cancer cases worldwide.

The BRU team hope this new plant-based technology could one day be used to test future HPV vaccines. First author of the study, Dr Renate Lamprecht, renateexplains: “We need pseudovirions to test any new HPV vaccine candidates. At the moment it is very expensive to make pseudovirions – we need to make them in mammalian cell culture, it needs to be sterile, and the reagents are very expensive.”

All these factors contribute to the high cost of current HPV vaccines, which are actually virus-like particles. Virus-like particles (VLPs) are similar to pseudovirions, but they contain no DNA. Plant- made pseudovirions, as demonstrated by this study, could reduce the cost of testing and manufacturing such vaccines, thus helping to make HPV vaccines affordable where they are needed most: the developing world.


Plant-made HPV pseudovirions containing geminivirus-derived DNA

The BRU team compared these new plant-made pseudovirions against the more widely-used mammalian cell culture-produced particles by using what’s known as a neutralisation assay. In this test (which is commonly used to test new HPV vaccine candidates), cells are ‘infected’ with pseudovirions, with or without pre-treatment with neutralising antibodies. The DNA inside the pseudovirion carries a ‘reporter gene’ that produces a protein that can give off a light signal. Thus, an infectious pseudovirion gets into the cell and gives off light, but one that is stopped by neutralising antibodies does not.

“I was jumping up and down the first time I saw the neutralisation results, but I repeated the experiment a few times to be sure, asking myself, ‘is everything correct, are all the controls there?’” explains Lamprecht. “It was a very exciting moment for us when we confirmed that neutralisation had occurred.”

Right now, every laboratory makes pseudovirions for such neutralisation experiments themselves. Dr Hitzeroth hopes that one day, they won’t have to: “we’re in the initial stages, but if we optimise the process and get the yield much higher, we think it’s a product that could be sold all over the world.”

ed ebola

Ed’s Ebola shirt

For Professor Ed Rybicki, Director of the BRU, this achievement was enormously satisfying, as it brought together two strands of his research interests that have co-existed for over 20 years.

“Seventeen years ago, I had the idea to combine making HPV VLPs in plants with a DNA plant virus we were working on, to see if we could make pseudovirions. It took until now for the technology to finally come together, but it shows what can happen in biotechnology if you’re willing to persevere.”

The BRU are also hoping to use this technology to create a therapeutic vaccine, which would also be a first of its kind. The idea would be to use the pseudovirion to deliver DNA that could treat an ongoing HPV infection or even a tumour.

With global acceptance and support for the biopharming movement growing rapidly, it might not be too long before the first plant-produced HPV vaccine is making a difference in Africa and around the world.”

For further enquiries, contact Dr Hitzeroth. For more info on biopharming, check out this Q&A session from Sense About Science.

“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.

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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

“Plant cell pack” workshop

23 November, 2015

As molecular farmers, we were much impressed last year by a technology developed by the folk at the Fraunhofer IME in Aachen: this is “METHOD FOR THE GENERATION AND CULTIVATION OF A PLANT CELL PACK“, with Thomas Rademacher as sole inventor on the patent application.  Basically, this involves

  • making a “cookie” or cell pack with cultured plant cells, by suction of a suspension onto a membrane
  • drizzling recombinant Agrobacterium tumefaciens onto the cookie, then sucking away excess fluid
  • incubating the cell cookie in a humid environment for a few days, until the desired level of protein expression has been reached

There are all sorts of things one could dream up for the application of this technology, given that one can make cookies of all sorts of depths and widths, in everything from spin columns to multiwell plates – and high-throughput screening of expression constructs comes to mind immediately.

Now fortunately, Inga Hitzeroth of our Biopharming Research Unit here at UCT (the BRU) has a National Research Foundation-administered bilateral grant with the folk at the Fraunhofer IME, which has meant we have money for joint workshops and the like – so we are having a hands-on Workshop on “Plant Cell Packs for Transient Expression: Innovating the Field of Molecular Biopharming” affiliated to our “Virology Africa 2015” conference next week.  We plan to develop an illustrated manual along with a full suite of technical tips after the Workshop.

And as part of which, one has of course to feed and entertain the participants – hence our expedition to The Spice Route wine farm complex yesterday.  Hard work, this science…B-)

The BRU-IME Cookie Workshop team: from left; Romana Yanez (BRU), Tanja Holland, Susanne Bethke, Markus Sack, Juergen Drossard, Gueven Edgu all IME), Ed Rybicki (BRU)

The BRU-IME Cookie Workshop team: from left; Romana Yanez (BRU), Tanja Holland, Susanne Bethke, Markus Sack, Juergen Drossard, Gueven Edgu (all IME), Ed Rybicki (BRU)



So that’s what you lot like, is it?

21 October, 2015


Don’t fear GMOs – fear the hype!

31 July, 2015
I’m going to share a slightly disturbing exchange I just had with a dietician – because it shows that even well-educated people out there are buying into the anti-GMO frenzy.

And I will thank +Mary Mangan for pointing out some of the sites mentioned!

“Dear xxxx;

In answer to your statements and questions:

“For a while, I have had the suspicion that GMO foods might be related to the epidemic increase in allergies, worldwide”

Ummmm…there is no good evidence of a worldwide epidemic of allergies – like autism, there is better recognition of the state, rather than an increase in incidence.

“my two boys clinically react to GMO varients,”

WHICH variants?  Of what?  How do you know?  This is a dangerous path, and I have trod it with immunologists involved in this sort of research – the ONLY way you can say “it is due to a GM food” is if you have the EXACT equivalent that is NOT GM – and by that, I don’t mean “GM vs non-GM maize” – because that is not biologically equivalent unless you have the same exact variety.  The other way would be to isolate the proteins involved, and test them – which is not that difficult, and is something I have thought of doing, if only to settle this issue for once and for all.

I would strongly urge you…to look at the links I will list below: most people, and medics and non-plant scientists as well, really don’t understand what actually happens with modern GM.  What happens is that one or a very few genes are introduced into a plant, to make one or possibly two proteins – against the 40 000+ the plant already makes. The genetic modification is minimal compared to conventional or advanced breeding, which moves around whole chromosomes, and MUCH easier to track than use of irradiation, which is also used to change traits – and very often changes things you can’t see and therefore ignore, unlike GM techniques.

What is more, all of the changes induced in plants can be followed these days by techniques like whole genome sequencing and proteomics, so that we can genuinely put hand on heart and say “this is exactly equivalent to that, except for one protein”.  Seriously: the question of equivalence is no longer really up for discussion; it is subject to evidence – and I will point out that the standards expected for GM plants are FAR more stringent than for conventionally-bred plants, which may have far bigger changes in protein composition than any GM variety.

I hope this is helpful!



Creating more effective vaccines against flu virus

4 July, 2015

Flu vaccines can be something of a shot in the dark. Not only must they be given yearly, there’s no guarantee the strains against which they protect will be the ones circulating once the season arrives. New research by Rockefeller University scientists and their colleagues suggests it may be possible to harness a previously unknown mechanism within the immune system to create more effective and efficient vaccines against this ever-mutating virus.

Sourced through from:

So: antibody-antigen complexes work better than antigen alone – and sialylation of the antibody is important.  Vaccinology really is entering the 21st century!

See on Scoop.itVirology News