GoF (pt2)

Before I revisit GoF (which I guess is admittedly, something of a hobbyhorse of mine), I must plug the BDG’s recent podcast on Euthanasia. Many thanks to the large (14+?)  group that gathered to eat my doughnuts and then discuss a difficult topic.

Anyway … on to a topic which I think  in some ways just as important but sadly, one that frankly, I don’t see is being discussed particularly rationally. Why is GoF so important an issue for me? I think it indicates a growing divide between scientists who do science, scientists who now no longer do science but earn a dollar commenting on science and politicians who have never done science but control the purse strings.

OK, GoF stands for Gain of Function and research using this technique has become increasingly controversial and something of a scientific football. Essentially, molecular biologists tinker with a pathogen’s genes and enable that pathogen to do “more”. That could include a wider host range (a non-human to human virus), different transmissibility (non-airborne to airborne) and so on.

Why are these experiments performed? Current medical countermeasures are often insufficient largely because of resistance mechanisms. There is, therefore, a continual need to develop new antiviral drugs and additional options, such as immunotherapy. GoF studies, which enhance viral yield and immunogenicity, are clearly going to aid the development of vaccines and other antivirals. How do we begin to study pathogens that only infect humans and have no animal models?

A recent PNAS paper (Menachery et al) describe a methodology involving a number of approaches to assess the ability of SARS-CoV–like viruses to infect human cells and cause disease in mouse models. The authors’ results suggest that a bat SARS-like virus, WIV1-CoV, can infect human cells but is attenuated in mice. Moreover, they indicate that additional changes in the WIV1-CoV genome would be required to increase the pathogenesis of the virus for mice. Vincent Racaniello (Professor in Microbiology at Columbia and one of the hosts of the fabulous TWiV podcast) was asked to write a commentary on the paper (see below) and again, criticised the current pause on GoF experiments. Essentially, Racaniello (and many others) want these studies to go ahead but more importantly want a balanced and informed debate to decide on the future of these experiments. Ideally, out of a series of debates and what would undoubtedly be some heated exchanges, a set of criteria would be agreed such that a panel could approve (or not) each and every GoF based on merit and potential risk. I won’t try and summarise Racaniello’s commentary, it is one I whole heartedly agree with. My worry is that large swathes of what might be considered “pure research” are already difficult to get funded because of a sometimes rather uninformed group of politicians who control the purse-strings. GoF undoubtedly has risks but surely the most prudent course of action would be to debate, discuss and then reach a decision. Pausing potentially valuable research without any plan to evaluate its benefits is surely rather reactionary?

Sadly, Wain-Hobson and others who stress some rather apocalyptic scenarios, currently have the upper hand. The sometimes angry exchanges between various camps may well be exciting but ultimately, given no international/multidisciplinary meeting is on the cards, it’s all rather sad.

Anyway, Racaniello’s commentary:

“The current government pause on these gain-of-function experiments was brought about in part by several vocal critics who feel that the risks of this work outweigh potential benefits. On multiple occasions these individuals have indicated that some of the SARS-CoV work discussed in the Menachery et al. article is of no merit. … These findings provide clear experimental paths for developing monoclonal antibodies and vaccines that could be used should another CoV begin to infect humans. The critics of gain-of-function experiments frequently cite apocalyptic scenarios involving the release of altered viruses and subsequent catastrophic effects on humans. Such statements represent personal opinions that are simply meant to scare the public and push us toward unneeded regulation. Virologists have been manipulating viruses for years—this author was the first to produce, 35 y ago, an infectious DNA clone of an animal virus—and no altered virus has gone on to cause an epidemic in humans. Although there have been recent lapses in high-containment biological facilities, none have resulted in harm, and work has gone on for years in many other facilities without incident. I understand that none of these arguments tell us what will happen in the future, but these are the data that we have to calculate risk, and it appears to be very low. As shown by Menacherry et al. in PNAS, the benefits are considerable.

A major goal of life science research is to improve human health, and prohibiting experiments because they may have some risk is contrary to this goal. Being overly cautious is not without its own risks, as we may not develop the advances needed to not only identify future pandemic viruses and develop methods to prevent and control disease, but to develop a basic understanding of pathogenesis that guides prevention. These are just some of the beneficial outcomes that we can predict. There are many examples of how science has progressed in areas that were never anticipated, the so-called serendipity of science. Examples abound, including the discovery of restriction enzymes that helped fuel the biotechnology revolution, and the development of the powerful CRISPR/Cas9 gene-editing technology from its obscure origins as a bacterial defense system.

Banning certain types of potentially risky experiments is short sighted and impedes the potential of science to improve human health. Rather than banning experiments, such as those described by Menachery et al., measures should be put in place to allow their safe conduct. In this way science’s full benefits for society can be realized, unfettered by artificial boundaries.”

Casadevall.A., 2014 mBio 5(4) “Risks and benefits of gain-of-function experiments with pathogens of pandemic potential, such as influenza virus: a call for a science-based discussion.”

Menachery.V.D., Yount Jr. B.L., Sims.A.C., Debbink.K., Agnihothram.S.S., Gralinski.L.E., Graham.R.L., Scobey.T., Plante. J.A., Royal.S.R., Swanstrom.J., Sheahan.T.P., Pickles.R.J., Corti.D., Randell.S.H., Lanzavechia.A., Marasco.W.A., & Baris.R.S. 2016 PNAS “SARS-like WIV1-CoV poised for human emergence.”


Zika – Pt 1, some background

The rapid spread of Zika virus through the Americas, together with the association of infection with microcephaly and Guillain-Barré syndrome, propelled a somewhat unknown virus onto numerous front pages. The WGS Biology Discussion Group (BDG) recently discussed some of the background for its first podcast  to this flavivirus but a little more background may help set the context of what is going to be an intriguing story for months to come.
Zika virus was first identified in 1947 in a sentinel monkey that was being used to monitor for the presence of yellow fever virus (another flavivirus) in the Zika Forest of Uganda. At this time cell lines were not available for studying viruses, so serum from the febrile monkey was inoculated intracerebrally into mice. All the mice became sick, and the virus isolated from their brains was called Zika virus. The same virus was subsequently isolated from Aedes africanus mosquitoes in the Zika forest.

Serological studies done in the 1950s showed that humans carried antibodies against Zika virus, and the virus was isolated from humans in Nigeria in 1968. Subsequent serological studies revealed evidence of infection in other African countries, including Uganda, Tanzania, Egypt, Central African Republic, Sierra Leone, and Gabon, as well as Asia (India, Malaysia, Philippines, Thailand, Vietnam, Indonesia).

Zika virus moved outside of Africa and Asia in 2007 and 2013 with outbreaks in Yap Island and French Polynesia, respectively. The first cases in the Americas were detected in Brazil in May 2015. The virus circulating in Brazil is an Asian genotype, possibly imported during the World Cup of 2014. As of this writing Zika virus has spread to 23 countries in the Americas.

The virus
Zika virus is a member of the flavivirus family, which also includes yellow fever virus, dengue virus, Japanese encephalitis virus, and West Nile virus. The genome is a ~10.8 kilobase, positive strand RNA enclosed in a capsid and surrounded by a membrane. The envelope (E) glycoprotein, embedded in the membrane, allows attachment of the virus particle to the host cell receptor to initiate infection. As for other flaviviruses, antibodies against the E glycoprotein are likely important for protection against infection.

Zika virus is transmitted among humans by mosquito bites. The virus has been found in various mosquitoes of the Aedes genus, including Aedes africanusAedes apicoargenteusAedes leuteocephalusAedes aegyptiAedes vitattus, and Aedes furcifer.Aedes albopictus was identified as the primary vector for Zika virus transmission in the Gabon outbreak of 2007. Whether there are non-human reservoirs for Zika virus has not been established.

Signs and Symptoms
Most individuals infected with Zika virus experience mild or no symptoms. About 25% of infected people develop symptoms 2-10 days after infection, including rash, fever, joint pain, red eyes, and headache. Recovery is usually complete and fatalities are rare.

Two conditions associated with Zika virus infection have made the outbreak potentially more serious. The first is development of Guillain-Barré syndrome, which is a progressive muscle weakness due to damage of the peripheral nervous system. The association of Guillain-Barré was first noted in French Polynesia during a 2013 outbreak.

Congenital microcephaly has been associated with Zika virus infection in Brazil. While there are other causes of microcephaly, there has been a surge in the number of cases during the Zika virus outbreak in that country. Whether or not Zika virus infection is responsible for this birth defect is not known. One report has questioned the surge (1) in microcephaly, suggesting that it is largely attributed to an ‘awareness’ effect.

Current epidemiological data are perhaps insufficient to prove a link of microcephaly with Zika virus infection. However the evidence establishing a causal relationship between Zika and microcephaly is growing as has the body of evidence that demonstrates that Zika could be one of the few pathogens able to cross the placental barrier and infect a foetus.

Given the serious nature of Guillain-Barré and microcephaly, it is prudent for pregnant women to either avoid travel to areas that are endemic for Zika virus infection, or to take measures to reduce exposure to mosquitoes.

There are currently no antiviral drugs or vaccines that can be used to treat or prevent infection with Zika virus. We do have a safe and effective vaccine against another flavivirus, yellow fever virus. Substituting the gene encoding the yellow fever E glycoprotein with that from Zika virus might be a good approach to quickly making a Zika vaccine. However testing of such a vaccine candidate might require several years.

Mosquito control is the only option for restricting Zika virus infection. Measures such as wearing clothes that cover much of the body, sleeping under a bed net, and making sure that breeding sites for mosquitoes (standing water in pots and used tires) are eliminated are examples. Reducing mosquito populations with insecticides may also help to reduce the risk of infection.

Oxitec first unveiled (2) its large-scale, genetically-modified mosquito farm in Brazil in July 2012, with the goal of reducing “the incidence of dengue fever,” as The Disease Daily reported (3). Dengue fever is spread by the same Aedes mosquitoes which spread the Zika virus — and though they “cannot fly more than 400 meters,” WHO stated, “it may inadvertently be transported by humans from one place to another.” By July 2015, shortly after the GM mosquitoes were first released into the wild in Juazeiro, Brazil, Oxitec proudly announced (4) they had “successfully controlled the Aedes aegyptimosquito that spreads dengue fever, chikungunya and zika virus, by reducing the target population by more than 90%.”

Closing thoughts
It is not surprising that Zika virus has spread extensively throughout the Americas. This area not only harbours mosquito species that can transmit the virus, but there is little population immunity to infection. Infections are likely to continue in these areas, hence it is important to determine whether or not Zika virus infection has serious consequences. Moreover evidence suggests that humans may act as an amplifying host for Zika (unlike Dengue for example) and thus person-mosquito-person transmission may be very common, hence a rapid spread into and throughout urban areas.

Recently, Zika virus was identified in multiple US states, including Texas, New York, and New Jersey, in international travellers returning to the US . Such isolations are likely to continue as long as infections occur elsewhere. Whether or not the virus becomes established in the US is a matter of conjecture. West Nile virus, which is spread by culecine mosquitoes, entered the US in 1999 and rapidly spread across the country. In contrast, Dengue virus, which is spread by Aedes mosquitoes, has not become endemic in the US.

What I have been fascinated by is the tone adopted by different public health and microbiology “camps”. Articles by numerous highly specialised scientists have both urged caution before we conclusively state that “Zika causes microcephaly” and warned us that Zika is the new Ebola only much much worse. Personally, I always thought that good science is evidence-based and a good scientist attempts to educate not frighten and always, ALWAYS adopts a moderate open-minded approach. Based on some of the salaries that contributors to the popular press on both sides of “the pond” enjoy, I’ve clearly been doing it wrong for years.


  1. http://www.nature.com/news/zika-virus-brazil-s-surge-in-small-headed-babies-questioned-by-report-1.19259
  2. http://www.oxitec.com/press-release-oxitec-mosquito-works-to-control-aedes-aegypti-in-dengue-hotspo/
  3. http://www.healthmap.org/site/diseasedaily/article/brazil-rolls-out-gm-mosquito-farms-71812
  4. http://www.iflscience.com/plants-and-animals/dengue-fighting-mosquitoes-are-suppressing-wild-populations-brazil

The Rise and Demise of Antibiotics

On the 20th of January Dr Chris Morris from the University of East Anglia delivered a talk to a keen audience of WGS Biologists and general science enthusiasts alike.

Dr Morris explained the ingenious method which he hopes will eventually lead to a new breed of antibiotics. Antibiotics in circulation today use a variety of methods to kill the bacterial cell causing infection – prevent the construction of the cell wall of the bacteria, stopping protein synthesis, prevent the bacteria multiplying, or allow the host’s defence mechanism to deal with it. The new method proposed by Dr Morris and his team was simple in concept, but as he later explained was much more complex in practise.

Segments of sense (coding strand) DNA are surrounded by a capsule of nanoparticles measuring between 1 and 100 nanometers in size. This capsule locates the bacteria being targeted by electrostatic forces of attractions and locks onto the bacteria cell surface. When attached, it punches a hole and the sense DNA fragment is released into the cell. Once inside the cell, the DNA segment knocks out a transcription factor – a protein that binds to specific DNA sequences, thereby controlling the rate of transcription of genetic information from DNA to messenger RNA – resulting in the repair response gene being switched off. The repair response to the hole formed in the surface of the bacterial cell no longer occurs, and thus by lysis the cell is destroyed. I believe it’s fair to say the audience were stunned by Dr Morris’ astounding method of puncturing the cell, and preventing the repair response as a way to remove bacterial infections.

Dr Morris also detailed some of the remaining hurdles to be overcome. One problem that continues is the control of the size of the nano particles and prevent the coagulation of them. Dr Morris is hopeful with more years of testing and hard work this form of antibiotic may one day be prescribed to patients fighting bacterial infections. His team’s method also raises the obvious question, is there any way we could apply this to the fight against viral infections?

Isabelle Hall