Thursday, December 29, 2016

What has Andy Wakefield done for science?

With the resurgence of Andy Wakefield through his "documentary" Vaxxed, his prior work has come back into focus. It's clear that his work as a researcher contains many errors of omission and commission, but why is the scientific community certain that something nefarious happened in his prior work? There is of course the excellent work from Brian Deer showing how the paper published in The Lancet was fraught with fraud and undisclosed conflicts of interest (being paid nearly a half a million pounds to show that the MMR is dangerous is kind of a conflict of interest). That investigation led to Andy losing his medical licence in the UK. However, much of the focus has been on the 1998 Lancet paper and not as much on his other work. I'll discuss one of his other papers here as it is incredibly clear that at best, inept data analysis and sample handling was done.   

In 2002, Andy was an author on a paper entitled "Potential viral pathogenic mechanism for new variant inflammatory bowel disease" published in Molecular Pathology (the PubMed Central deposit can be found here). The paper uses qPCR detection of the Measles virus using the Taqman chemistry (see image below). 


This is how Taqman qPCR works.

The results of the paper look normal to the lay person; however, if a researcher who is familiar with qPCR looks at the raw data from the paper, an enormous problem is evident. I rarely share youtube videos; however, this video from C0nc0rdance explains qPCR and why the issue is such a huge deal.


For those who don't want to watch the video, the problem is simple. qPCR is done using a thermocycler that uses a laser to detect a fluorescent target and is linked to a computer. The software on the computer automatically does calculations for determining what is positive and what is not. One of the calculations that is done is the threshold for determining what is considered a positive reaction and what is not. In the 2002 study, the threshold was manually lowered so that samples that should have been negative came up as positive. These samples were all after cycle 30 which means that it was a small quantity of material being detected. Additional analysis of the raw data by Dr. Bustin (an expert on qPCR) found that these were false positives due to contamination. So we have two major issues to contend with here. First the samples were contaminated (qPCR is sensitive to contamination so extra care has to be taken to prevent this). Second, the data was improperly analyzed and the Ct threshold improperly lowered so that these samples became positive. At best, this is poorly conducted science that should be retracted. At worst, if the threshold was knowingly altered to generate positives, this would be scientific misconduct. It's not likely that the contamination was intentional as it was in low quantities (why spike a sample with an amount that would look like contamination rather than spike with an amount that would clearly be positive?) and some of the researchers involved in this study published a subsequent study that found no measles virus when the experiment was replicated (three independent labs did the tests on each of the samples), so the adjusted analysis was probably done in ignorance rather than malice.

But this paper (and several others) did have a positive impact on the scientific community. It lead to the creation of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE). These standards dictate what the minimum amount of information needs to be included with a paper using qPCR data. This includes information on how the samples were extracted, how the test was validated, what controls were used with the test, and how the data were analyzed. Many of the top journals have adopted these guidelines and many researchers follow them even if it isn't required for publication (it's just good science). 
Information needed to fulfill the MIQE guidelines.
So even though Andy Wakefield is at best an incompetent researcher (and a con artist at worst), he has done something good for science. As a result of his work (and the work of others), the standards for qPCR reporting have been increased so that the results are standardized across disciplines and publications. It does bring up an interesting question, how many of Wakefield's previous studies are faulty and what should be done about them. In this case, a correction should have been submitted, at the very least, when it became clear that the data analysis was not done properly and that the resulting conclusions are suspect. 

However, one thing is clear. Andy Wakefield is not the virtuous crusader for the truth that has been unfairly attacked by the forces of evil. Despite the narrative that he tells, his work speaks for itself. It is full of errors and improprieties that make it all suspect. His actions are what led to him being shunned by the scientific community. Andy shouldn't be blaming anyone but Andy. 

Saturday, December 3, 2016

Genetic modification of Influenza A virus reveal a novel vaccine production strategy

Researchers have developed a new type of vaccine. By genetically modifying the genome of Influenza A virus to require a non-standard amino acid (Ne-2-azidoethyloxycarbonyl-L-lysine which has been used in synthetic biology previously) that some microbes use. What makes this amino acid unique is its codon (three base RNA sequence that signals what the amino acid should be). In most organisms, the codon used (UAG) is actually what is known as a stop codon (it stops production of the protein chain), so this means that any gene that contains that codon will stop prematurely unless grown in an organism with that non-standard amino acid. A lot of work went into finding places in the viral protein that the non-standard amino acid could be inserted without interfering with the function of the protein. Once several sites were identified, the researchers grew the virus in kidney cells that had been genetically modified to use the non-standard amino acid. The end result was genetically stable progeny viruses that required the non-standard amino acid.

When the altered influenza virus was injected into mice, it did not replicate and the mice developed a strong immune response to the virus. Researchers were able to safely inject the mice with a dose of the modified virus that was about 100,000 times the dose of the wild-type virus that would kill half of the mice injected (LD50). The modified virus also interfered with the wild-type influenza virus in co-infections of the two.  

The implications for this development could be astounding. With this, researchers could develop a vaccine that uses a fully infectious virus that has been modified to need this amino acid to replicate. However, caution is warranted at this point. A lot of work still remains to develop this into a functional vaccine. It must go through further trials to see if it works in primates and then there are all the human clinical trials that are needed. This work is promising and certainly should be pursued further.


This negative stained transmission electron microscopic (TEM) image shows recreated 1918 influenza virions that were collected from supernatants of 1918-infected Madin-Darby Canine Kidney (MDCK) cells cultures 18 hours after infection. Photo credit: Cynthia Goldsmith courtesy of the CDC.

Friday, December 2, 2016

Poinsettias and pathogens



Poinsettias are a very interesting plant. Originally, this plant grows as either a small shrub or a tree in its native range (Mexico). However, the little potted poinsettias that can be bought at the store never grow close to that size. There is a good reason for this: the potted poinsettias are infected with a pathogen known as a phytoplasma. Phytoplasmas are small bacteria that lack a cell wall and are limited to the phloem tissue within plants. They are spread by vegetative propagation, grafting and by sap-sucking insects that feed in the phloem. Normally phytoplasmas are associated with severe disease in plants by altering the structure of plants, such as causing the petals of flowers to develop into leaves instead of petals. One such disease is aster yellows which infects over 300 different plant species in 38 families (see picture below).
Aster yellows on the Purple coneflower (Echinacea purpura). Via wikipedia
But what does this have to do with poinsettias? It turns out that the phytoplasma that infects the potted poinsettias also causes stunting, but doesn't cause severe distortion of the leaves. Not only is the plant stunted, but it produces additional branches where normally the plant has a single branch. The trait has been used since the 1920's to sell poinsettias during November/December in North America. This trait was found to be transferable by grafting but could be lost when the plant was subjected to heat treatment or tissue culture techniques. It was thought that another pathogen that is common in poinsettias was the cause of the stunting, Poinsettia mosaic virus, but it wasn't until the 1990's that a phytoplasma was shown to be the causal agent of the stunting. Previous work found that the virus wasn't completely associated with this trait as plants without the virus developed stunting and free branching. This article contains further information on the history of poinsettias and the work to determine why commercial poinsettias are stunted and free branching. This article discusses how to care for poinsettias.

A poinsettia tree in Mexico. Via Petal Passion

A potted poinsettia. Via pixabay.


The phytoplasma infecting poinsettias is a perfect example of how not all pathogenic organisms are bad and that they might be of benefit. This is certainly the case in the ornamental industry as it is the basis of the entire ornamental poinsettia industry.

Wednesday, November 2, 2016

Does Zika damage the testicles? Maybe

A lab mouse. Picture via Pixabay

A new study is causing quite the stir. Researchers used a mouse-adapted African strain of Zika to examine if the virus damages the testicles, as Zika has been detected in the sperm for up to 10 weeks post infection. In this latest study, severe damage and significantly smaller testicles were observed in infected mice. By day 21 the damage was much more extensive. Starting at day 14, sperm count and sperm motility dropped and by day 42, the differences were large. Overall, the fertility of infected mice dropped from around 80% to roughly 25% and the number of viable fetuses from the sperm of infected males dropped from 25 (from uninfected sperm) to 10. The researchers also tested this with mice infected with Dengue and an isolate of the Asian strain of Zika, but Dengue didn't damage the testes and the Asian strain caused less damage. The researchers hypothesize that the difference seen between the African and Asian strains is due to the Asian strain not being adapted to mice whereas the African strain was (it replicated less efficiently than the African strain in the mouse model).

Mouse testicles either infected with Zika or not, after 7 (a), 14 (b) or 21 days (c) post infection. Adapted from Govero et al., 2016; doi: 10.1038/nature20556

This study, although valuable, does have some limitations. First, a mouse-adapted strain was used which could result in mutations that make the virus different than the ones circulating in humans. Second, the work was done in a mouse model and sometimes research in mice doesn't translate to humans. However, this was just a preliminary study and something of concern was noted. These findings more than justify further work to examine if Zika causes damage to human testicles and if it can reduce fertility. 

Saturday, October 29, 2016

Zika causes birth defects (another case of Moms Across America ignoring science for ideology)

A friend of mine (Iida from Thoughtscapism <FB; website> sent me an interesting story that seems to be gaining steam in the anti-GMO world: Zika doesn't cause birth defects. Before I get started on debunking their claims, it's important to give a proper background on what Moms Across America truly represents and why they are not a valid source of information on anything related to science.

Moms Across America started off as an organization that was opposed to genetically engineered crops (colloquially known as GMOs). They rabidly oppose agrochemicals (glyphosate is a favorite target of theirs) and are well known for outrageous claims that they found glyphosate in X substance. They have claimed to find it in breastmilk, wine, granola bars and more recently vaccines. The group has recently branched out as being opposed to vaccines (although in all fairness, Zen said this was her personal belief and not necessarily the views of the organization), they have acted as a lobby wing and advertiser for organic food, and it now appears to be anti-science in general with their latest post. Researchers have taken the time to look at the methods used in the case of their breastmilk-glyphosate study and even tried to replicate it using proper testing protocols. They have also faced backlash for their attacks on breastfeeding (apparently to help market non-GMO formula, or rather that is what some suggest) and for parent-shaming those who do not "care" enough to feed their kids organic foods. In short, the positions of this group tend to be opposed to science and favor bad science over well designed and accurate studies and science. 

So what does this have to do with Zika and birth defects? In Zen's latest anti-science article she makes a series of claims (sourced from one Ian Trottier) that have no basis in science. She blames the "overblown" hysteria around Zika for allowing $1.9 billion in taxpayer dollars to go to Big Pharma for vaccines and Big Chemical for pesticides. Naturally, in her mind both vaccines and pesticides are far more dangerous than a virus, despite all the evidence to the contrary. First, I'll discuss her "evidence" and the four points that she tries to use to prove that Zika isn't a danger and then I'll discuss what the actual scientific evidence is for Zika causing birth defects (as she wrongly claims that there is no science to back up the idea that Zika causes birth defects). 

In the article, Zen tries to link to several "sources" to claim that Zika doesn't cause birth defects. The first link claims to have all sorts of evidence from science journals that Zika does not cause birth defects. This is what she says about the source: "The website sources articles from the New England Journal of Medicine, Lancet, PubMed, EPA, CDC and others. Additionally, site developer, Ian Hamilton Trottier, has conversed with experts at Lancaster University in the UK and the London School of Hygiene and Tropical Medicine. That includes experts based in the US." However, when you click the link you get the following:


Zen's first source that is "full" of scientific journal articles that "demonstrate" that Zika does not cause birth defects. 
Later in the article, she tries to cite MiamiCAN.org as a source. However, when you click on that link, it is for a domain that is for sale:


Zen's second attempt at linking a source for her claims.

The third source does list the four claims that Zen mentions in her article, but lacks any sources to back up the assertions. 


The fourth time seemed to be the charm as when MiamiCAN.com was linked, you get a website that has some sources. However, every source on that page deals with naled and does not back up the assertions that there is no credible scientific evidence that Zika causes birth defects. Furthermore, Zen claims that Dr. Michael Diamond "is essentially quoted as saying there is nothing that suggests detection of ZIKA as being the actual cause of MICROCEPHALY in the subjects he's studied. Dr Diamond recently published a review that links ZIKA to being present in tear ducts."
Dr. Diamond is indeed a flavivirus expert (the genus that Zika virus belongs to) and has published extensively on Zika (and other viruses and immunology in general). Since I cannot find the quote that Zen is alluding to and the fact that Dr. Diamond's work has been instrumental in confirming the link between Zika and birth defects, one is forced to assume that this quote is from the early days of the Zika outbreak in Brazil, when researchers did not know what we know now about Zika causing birth defects. This is a cherry picked quote that attempts to use an appeal to authority to confirm Zen's ideology despite the fact that the source has clearly demonstrated the opposite of what she is claiming.

The four points of the article basically boil down to "we don't know" and pesticides. She tries to link the use of the pesticides to both Monsanto and the Nazi bombing of France in a clear attempt to poison the well. Pesticides that have been ruled out as being involved with microcephaly, like 
pyriproxyfen, get mentioned as a possible cause. I won't get into that here as I've addressed pyripoxyfen before. It's sort of a rehashing of the claims that Mike Adams made about Zika that I also debunked previously, except Zen mentions paraoxonase as to why naled is really causing the birth defects attributed to Zika. However, her assertion that children have lower levels of paraoxonase in their liver does not automatically mean that the levels of this enzyme are the reason for birth defects. It ignores the fact that the mother's liver will help protect the growing baby. A study did find that lower maternal levels of one of the enzymes in this class did lead to a smaller head circumference, but it was nowhere near the level of reduction seen in babies born with congenital Zika disorder. I don't have the space to get further into the claims surrounding this enzyme as it is complicated.

But what about the evidence that supports the link between Zika infection during pregnancy and birth defects? How solid is the science on this? I'll outline just some of the key findings that support that Zika virus causes birth defects. The body of scientific literature is extensive on this topic and one only has to look to find it.


1) The Zika virus crosses the placental barrier
2) The complete genome of Zika has been recovered from the amniotic fluid and brain tissue of an infected fetus. 
3) Zika virus has been shown to disrupt brain organoid formation and deplete neural progenitor cells in vitro.
4) Case studies have shown a link between congenital Zika infection and birth defects.  
5) Zika virus infection caused birth defects in a mouse model. Specifically the Asian strain is more damaging than the African strain. 
6) A case-control study has demonstrated a clear link between congenital Zika virus infection and birth defects. 

Some of this work has been published since May 2016 when this article summarizing the evidence for congenital Zika virus infection and birth defects was published. This article concluded that the available evidence had met the criteria for a causal link to be established. Since then, the evidence supporting the link has only gotten stronger and at this point attempts to deny the link shows a clear lack of understanding of science. This infographic I made summarizes the evidence for Zika being a TORCH pathogen (TORCH pathogens cause birth defects).


The Zika virus is a TORCH pathogen that causes birth defects.

This article from Zen is a clear cut case of her ignoring the science that clearly demonstrates that the Zika virus causes birth defects. Although to be fair, it's entirely possible that she just doesn't understand the science. Based on her past history, that cannot be entirely discounted; however, not understanding science isn't an argument against it. The real moral here is that people need to be careful what they use as sources. Moms Across America, much like Natural News or Joseph Mercola, have clearly demonstrated that they are not a valid source when it comes to science. They cherry pick quotes and ignore all of the scientific evidence that contradicts their ideology. Moms Across America really shouldn't be used as a source for anything. 

Saturday, October 22, 2016

Sexual transmission of a bee virus


A queen honeybee. Via wiggledanceforme.


When sexually transmitted infections are discussed, one might think of human viruses, such as HIV or herpes. However, other organisms can become infected with viruses from sex. A new study describes how one of the more debilitating bee viruses, Deformed Wing Virus (DWV), can be sexually transmitted from infected male drones to otherwise healthy queens after mating. As the name might suggest, DWV severely deforms the wings of infected bees (see picture below) and impairs their cognitive function, specifically impairing the learning behavior and memory retention. Because of this, it wasn't known if infected drones would be successful at mating or not.

Carniolan honey bee with Deformed wing virus. Photo credit, Xolani90, via Wikipedia. 

In order to test this, the researchers took extensive steps to ensure that queen honeybees were free of viruses. They came from the same virus-tested colony as larvae and were then reared in nurse colonies that lacked a queen. That colony was screened for the varroa mite (300 bees were examined and none had the mite) and common bee viruses tested for in 60 worker bees. These include DWV, Black Queen Cell Virus, Sacbrood Virus, Chronic Bee Paralysis Virus and the ABPV complex made up of Acute Bee Paralysis Virus, Kashmir Bee Virus and Israeli Acute Paralysis Virus. A total of 30 queens met this criteria and were used in the study. They were then allowed to mate with DWV-infected male drones for at least 7 min; nine did not mate for the full time leaving 21 queens that fulfilled the requirements. If the drone's endophallus was still present in the queen after mating, then it was removed and tested for DWV; three of these had high levels of DWV. They found that seven of the queens developed high levels of systemic DWV infection; one of these queens died shortly after ovipositing (laying eggs) due to the infection. A further 15 queens had medium levels of DWV that varied in titer by tissue and eight queens had low levels of DWV.

This study answers an important question: can DWV-infected drones pass the virus on to queens by mating? The answer is a clear yes. Part of the reason why this study is important is because DWV is one of the major viruses associated with colony collapse disorder. Complicating matters, previous work has demonstrated that the varroa mite prefers drone brood (the varroa mite transmits all the viruses listed in this post to bees). 
Another issue is that if a queen dies, then the colony will be lost. Up to 25% of lost colonies are the result of loss of the queen. This new discovery could have implications for managing honeybees and lead to the development of strategies to mitigate these losses. 

Tuesday, October 18, 2016

Rift valley fever virus as a risk factor for miscarriage

Distribution of Rift valley fever virus via CDC.

New research has discovered that Rift valley fever virus(*more on this virus below) may be a risk factor for miscarriages. In a cross-sectional study of 130 pregnant women with fever in Sudan, it was found that 28 were infected with Rift valley fever virus and 31 with Chikungunya virus (also mosquito transmitted). In the women infected with Rift valley fever virus, 54% had a miscarriage compared to 12% in those not infected; this represents a 7-fold increase in miscarriage associated with the virus. Infection with Chikungunya virus did not result in a statistically significant increase in miscarriage, though the symptoms of this virus are quite unpleasant. The study does have some limitations, such as the smaller size, but these factors are hard to improve based on the system they are working with (it's not exactly ethical to infect large numbers of pregnant women with a virus to see if it causes miscarriages). However, this study does highlight how essential it is to try and prevent mosquito bites during pregnancy as there are several viruses of concern for pregnant women (such as Zika).




*Rift valley fever virus is a mosquito-transmitted virus in the genus Phlebovirus in the Bunyaviridae. It normally infects cattle and other domesticated animals, but also can be transmitted to humans, though this isn't as common; contact with infected animals is a known risk factor for this virus. The disease is normally mild, but in some cases, it can cause severe disease (1-3%). It is transmitted by Aedes species mosquitoes that also maintain the virus through vertical transmission (eggs are infected by the virus if the female mosquito is infected) but other mosquitoes can transmit the virus mechanically. The distribution is limited to Africa and the Middle East, but with the warming climate, researchers are worried that it could spread to new areas (as Aedes species mosquitoes like A. aegypti and A. albopictus are expanding their range) and one of the vector species is common in Europe. 

Monday, October 17, 2016

Misusing definitions is not the way to counter misinformation: Colony collapse disorder

European honeybee, Apis mellifera. Image via Wikipedia.


Anyone who has followed my page for awhile knows that one of my big pet peeves is bad science reporting. One of the ways that bad science reporting happens is when non-experts misuse definitions to draw incorrect conclusions. The best example of this is the reporting on colony collapse disorder (CCD). 

To give an example of some of the bad reporting around CCD, last year, Christopher Ingraham wrote an article for the Washington Post where he declared that the "beepocalypse" was over as the total number of hives has not gone down since CCD was first seen. To be fair, he's not the only one who has used this incorrect definition; Matt Miller used the same figures for his article in Slate. Their argument boils down to this: "Because the total number of hives haven't dropped means that the bees are doing just fine and any concerns about CCD are just overblown." This sounds like a fine conclusion until one realizes that they are not actually using a measurement that deals with CCD. When it comes to CCD, the total number of colonies does not matter. 

CCD is defined by the percentage of the adult bees that abandon the colony without leaving dead bodies in the hive while leaving brood and honey intact with the delayed invasion of the usual hive invaders (small hive beetle, wax moth, etc.). Typical losses in the winter range from 15-20%, so anything above 20% is classified as CCD. In 2014/15 the winter losses were 23.1%. However, the summer losses were much higher making the average losses for the year 42.1%. It's atypical to have high summer losses and it is very concerning. In 2015/16, the high summer losses continued with an average loss of 44% for the year. The losses the last two years are certainly above the threshold for CCD, so CCD is clearly still a problem. The article tried to gloss over it by using the wrong statistic and oversimplifying the problem. I find this distasteful as a science communicator as it misleads the public despite the issues with the authors argument being plain for those who are familiar with CCD.

In the comments on his article last year, Mr. Ingraham was taken to task by several beekeepers for his lack of understanding of CCD. However, rather than fact check his hypothesis by asking any entomologists or experts about it, he has doubled down with yet another article touting that the bees are just fine as the hive numbers are still high. He is facing yet more backlash in the comments. Some of them are incorrect and are lacking in any scientific basis. But not all of the comments were wrong. Several pointed out that the definition of CCD was being used incorrectly and that was leading to incorrect conclusions. One simply cannot try and disprove bad science by using bad science themselves. In science, definitions matter, especially if it is a disease or disorder that is being discussed. This is the same faulty understanding of science that leads people to question the effectiveness of vaccines or doubt that humans are contributing to the increasing global temperatures.   


But the problems with the article doesn't stop at misusing the definition of CCD. The author gives some solutions that are meant to negate the effect of CCD; however, neither solution is actually a long-term solution for CCD. From the article:

"So beekeepers have devised two main ways to replenish their stock. The first method involves splitting one healthy colony into two separate colonies: put half the bees into a new beehive, order them a new queen online (retail price: $25 or so), and voila: two healthy hives. The other method involves simply buying a bunch of bees to replace the ones you lost. You can buy 3 pounds of "packaged" bees, plus a queen, for about $100 or so."
There are several issues with the two solutions proposed. Splitting a sick or weak hive results in two sick/weak hives. It'll take time for each hive to build back up with a healthy hive that is split. Splitting weak hives is not a good solution. Buying more bees is just a temporary measure at best as eventually the hive will develop CCD if it's a commercial hive. Neither of these options really addresses what CCD is (remember, it's the loss of bees from a hive without dead bodies being near the hive), so these are akin to trying to put a band-aid on a serious wound. The author did get called out on this by several beekeepers, but their concerns weren't addressed and in fact he repeated these solutions in his second article.
An example of one of the comments from the article.

But what does it matter if one uses the wrong definition for CCD to discuss it or offers a solution that doesn't address the problem? CCD is still a major problem and is causing significant losses. What's worse is that if people truly believe what he is trying to say about CCD, funding for studying and ultimately finding a treatment for CCD could be in jeopardy. The solution of splitting hives or buying new bees isn't anything more than a temporary attempt at a solution. 
I get that this was an attempt to try and dispel the misinformation that surrounds CCD, but you cannot counter misinformation with more misinformation. 

But that doesn't mean that the bee situation is nearly as dire as some would have you believe. The reporting on the other side of the issue is equally atrocious. If we lost honeybees, there are other pollinators that are less efficient. Even if we lost pollinators altogether, we wouldn't starve. Almost all staple crops (wheat, corn, rice, potatoes, etc.) are either wind or self pollinated, so we wouldn't lose access to these food sources. We would lose many fruits and vegetables, such as apples, stone fruits and cucurbits, but we wouldn't starve. But this doesn't mean that losing the bees is something we should be okay with either. Bees play a huge role in agriculture and have for thousands of years. It would be a tremendous loss if they weren't around, even if it doesn't mean that we would starve.

I'll have a blog post soon discussing what some of the current research suggests is involved in causing CCD is. I'll give you a hint, viruses might be involved. But until then, there are some great places to get information on bees and CCD without having to wonder if the science is shaky. Scientific beekeeping is arguably one of the best resources for learning about the science of beekeeping and CCD. CCD is incredibly complex and there isn't a single definitive cause or easy solution for dealing with it. 

Saturday, October 8, 2016

Quantifying the harm that Zika does to unborn babies

Artificially colored EM image of the Zika virus. Credit: CDC


Last week on my page, I posted an article from NBC news about how Zika might be more damaging than we initially thought. Several people expressed concern that it was just a news article and not a scientific study. A study has now been released that quantifies the harm that Zika does and it is quite shocking. A little over a year ago, I posted about Zika on my page for the first time. I had come across an article detailing how Zika was potentially transmitted through sexual contact. This was unusual for an arthropod-borne virus and it caught my eye. Little did I know that Zika would then take center stage in the media as a result of another unique characteristic that it seemed to posses: causing birth defects. 

A newly published study has expanded what we know of the harm that Zika can cause in unborn babies, for which the author propose calling congenital Zika syndrome. Medical professionals in Brazil followed 11 babies that were born with congenital Zika syndrome and were confirmed to have been infected by the virus. From following these babies, the authors were able to categorize several neurological conditions beyond microcephaly that these babies suffered from. Of these 11 babies, three died from the syndrome within 48 hours of being born. Autopsies were performed on two of them and extensive damage to neural and brain tissue were seen. In some of the babies examined, it was found that the thalamus was calcified and in some cases absent. The thalamus is involved in the sensory systems and sleep & wakefulnessCalcification in brain tissue can lead to a myriad of problems that leads to dysfunction. Another problem seen was lissencephaly, or smoothing of the brain tissue, which also causes dysfunction. In addition to the neural disorders, arthrogryposis, or involuntary contraction of the joints.

In total, these data suggest that Zika may do more severe damage than initially thought. I didn't get into everything that the new study described as a result of Zika infection, but the totality of it is horrifying. The reports of the symptoms these babies have now makes sense when one sees the damage to the brain that this virus causes. This study helps make the case that Zika should be added to the TORCH acronym as its own entity due to the extent of the damage that it does. 





Tuesday, October 4, 2016

Publication by press release: When an HIV cure may not be a cure



I'm sure that many people have seen the news that a cure for HIV has been found; however, when you start digging into the claims, it is very clearly premature to declare this. It is true that a trial has begun to see if a chemotherapy drug, vorinostat, could be effective at helping the body to clear HIV with the aid of anti-retroviral therapy drugs. A total of 50 people are going to be in the trial and only one has completed treatment. The patient doesn't have HIV in their blood so the NIHR made a press release touting their "cure" and the media blew up with many sensational headlines. Once reporters had a chance to digest what was actually being said, calmer headlines have started to appear, including this excellent piece from BBC. I'll go through some of the finer points that need to be fully addressed before we can tout this a cure. 

The first is that they only tested this on people already undergoing HAART (highly active anti-retroviral treatment) treatment and had minimal detectable HIV titers. This hasn't really been tested in people with an active infection, only the integrated infection. The drug may not work in this scenario which would mean it's not a true cure. Looking further, the in vitro testing has only been done with latent infections and the drug does a good job of causing the latent virus to actively replicate. There is also no information on whether the virus can mutate so that this treatment is no longer effective. HIV mutation has been one of the main reasons that a cure for this virus has not been developed yet. Even the highly powerful CRISPR/Cas9 system was found to be susceptible to HIV mutation rendering it ineffective as tested.

A second major issue is that the people being treated continued with HAART while being treated with voinostat. This makes the results of the study difficult to interpret. HAART therapy causes the viral titers to be low as it interferes with the ability of the virus to replicate. Since they are measuring titer, they could potentially miss some latent infections (if this is indeed what they are doing; see the next point). 


The third major issue is that the trial is nowhere near complete. They have only recruited 39 out of 50 patients and the full results are not expected until 2018. This is a small pilot study that doesn't have the numbers to see how effective the treatment is, just if it can work or not. To be blunt, the press release was lean on specific measurements and methodologies, which is to be expected as it is not a paper but a press release. However, this makes it difficult to judge the way that the study was performed. 

A fourth issue is that only one person has completed the trial and they just finished. The researchers still need to test the patient for months to see if the therapy worked. Based on this and the previous three points, it is far too premature to call this a cure for HIV. The trend of publishing by press release is a growing trend that is not a welcome one. By issuing a press release, the normal peer review process is by passed, including post-publication peer review which is crucial to the process. Without the full methodologies or unbiased reporting of the results, there is no way for the scientific community to accurately judge the value of this work. In all fairness, I doubt the researchers had little say in the decision to give a press release. As it came from the funding agency, they likely seized on a promising report and used that to make the announcement.

Publication by press release is the bane of many researchers and has been of particular concern in HIV work. It seems that everyone rushing to cure this virus is using this method for disseminating findings. All too often, the sensational headlines announcing a particular technique as a cure do not live up to the hype that they have created. I'm sure that the drive to be the first to cure HIV is driving this. However, this is not based in the scientific method and it would be far better to have a solid cure that has gone through the rigors of the scientific method. Part of the reason for this is that every time a cure is announced, those suffering from this virus get their hopes up only to have them crushed yet again. To me, this is worse than just reporting that a treatment didn't work. The toll on people's health is real and this is not okay.

Update: A page called HIVforum.info shared the registration information on the clinical trial that includes some details about methods used in the trial. There still are questions, such as what method they are using to asses HIV DNA and if they are checking for integration beyond that or not, but this does give us more clues to what they are doing.

Sunday, October 2, 2016

Zika Update 10-2-2016


Aedes aegypti


It's been a busy two weeks with news on Zika. As usual, there is good news and not so good news.

First the best news: The US congress has finally approved the Zika spending bill and the important research that was in danger of running out of funding. However, the delay in funding has allowed Zika to establish a foot hold in the continental US and resulting in money being used to develop strategies to combat Ebola being diverted for the Zika work. 


There is more good news for Zika with a vaccine entering Phase I human trials now. Another piece of good news was the identification of a co-factor that increases the risk of birth defects: prior infection with Herpes simplex virus-2 which I wrote a blog post about here.

Now for some of the bad news. It is now likely that Zika can be transmitted by sweat and tears. This is the result from the case in Utah where someone was infected caring for an infected family member who later died. As a precaution, people who are caring for those who are sick with Zika should make sure that they are careful and not coming into contact with bodily fluids that may contain Zika. Likewise, new recommendations from the CDC advise that those exposed to Zika but aren't showing symptoms wait 6 months before trying to have children (or unprotected sex with a pregnant woman). The previous recommendation was 8 weeks. 

In more bad news, the area of local Zika transmission is expanding with more mosquitoes being found outside of the original area 
that are carrying the virus. Likewise, more cases are being reported in the area from both local sources and from travel. If this news wasn't bad enough, local surveillance of mosquitoes has revealed that Dengue is now in Southern Florida as well. This is bad news because research has revealed that Zika and Dengue are closely related enough that they can cause antibody-dependent enhancement of disease. This means that getting Dengue first could result in a more severe case of Zika infection and that getting Zika first could result in the more severe form of Dengue that can be lethal.  

We are also beginning to discover that Zika causes more lasting damage in children infected in utero than researchers initially thought. The initial reports are just starting to come in, but it may be years before we know the full extent of damage that Zika does. This damage highlights why a vaccine would be warranted even if the rate of birth defects are low. Additionally, cases of birth defects caused by Zika are being seen in other locations, outside of Brazil, where outbreaks are occurring. Two cases of microcephaly have recently been identified in Thailand that have been linked to Zika infection. One argument that is commonly used against Zika causing birth defects is that cases of microcephaly haven't been seen elsewhere. This wasn't the case prior and now that researchers and medical professionals know what to look for, cases are being identified in locations with outbreaks.

Another sad result is the recent fight between researchers over the best test for detection of Zika. In recently released documents, a researcher has been fighting with the CDC over whether using an RT-PCR test (used to detect RNA viruses) in singleplex (targets only one sequence) or a multiplex (targets two or more unique sequences) assay is best. Fights like this only hurt public confidence as the nuances that would be plainly evident to researchers are not known by the general public. Yes, testing for a single target at a time is generally more sensitive than multiplexing several targets; however, multiplex assays can be optimized so that is isn't an issue and should be done prior to releasing the technique to the community. But this fight is something really belongs in a scientific journal and not on the internet.


In an interesting piece of news, a team from KSU recently reported that Culex species of mosquitoes do not transmit Zika. However, there are a number of issues with this report. They didn't actually test for transmission, they just fed mosquitoes infected blood and tested them by RT-PCR after 7 and 14 days. None of the mosquitoes tested positive after 7 days despite being positive immediately after feeding. There are a number of concerns that are raised by the methodology used in this study. The first is that they only tested a small number of mosquitoes (about 30 at each time point for two isolates of C. pipiens and one of C. quinquefasciatus). I reported in the last update that C. pipiens is not a vector as seen in a transmission assay (really the best way to see if an arthropod is a vector or not), so I don't doubt those results. If C. quinquefasciatus is an inefficient vector, it is possible to miss it with those numbers. Another issue here is that there is a conflicting report from Brazil where replication of Zika was detected in several tissues including the salivary glands (which is a prerequisite to transmission for flaviviruses). In the report from Brazil, a total of 99 mosquitoes were tested which could explain the differences between the two studies. Another big difference is the study from Brazil used qRT-PCR as opposed to RT-PCR (qRT-PCR is far more sensitive than RT-PCR). Additionally, electron microscopy was done on the dissected C. quinquefasciatus salivary glands and signs of viral replication were observed. More importantly, this work from Brazil showed that Zika had low titers in C. quinquefasciatus, suggesting that there is the risk of RT-PCR detection resulting in false negatives due to the low starting titer. Certainly more work is needed here, but the results of the Kansas study do not show that C. quinquefasciatus isn't a vector for Zika as they never tested that. That is bad science reporting and could lead to serious repercussions as a potential vector could be ignored.

I didn't want to leave this update on a sour note, so I saved one of the best stories for last. A paper describing two Zika DNA vaccines (see my infographic below) has been published. In addition to these vaccines protecting mice and eliciting a robust neutralizing antibody response in rhesus macaques, the results  give researchers a clue as to the dosage needed in order to prevent viremia (spread of the virus through the bloodstream). One of these DNA vaccines is currently the one that is in clinical trials that I mentioned above. The second DNA vaccine will start Phase I clinical trials soon. 


My infographic on DNA vaccines.

Thursday, September 29, 2016

When to get the flu vaccine and why bad science reporting hurts people

An infographic I made to address what effectiveness means.

Anyone who's followed my page for awhile knows how much I dislike bad science reporting. I don't know if it's been a slow news day or what, but several news outlets have run a story with a headline that is misleading and may make some question getting the flu vaccine. The article, "Getting a flu shot? It may be better to wait," poses the question if people should wait to get the flu vaccine or not. They argue that since the flu vaccine loses effectiveness as the season progresses that people should delay getting it. I should note that vaccine effectiveness only measures the prevention of infection and doesn't include the reduction in symptom severity, disease duration or the number of hospitalizations that are seen with the vaccine. The problem with this is that the argument is based on a single study from a region in Spain when the flu season was atypical. The season started later than normal and the strains circulating in that region of Spain were different than what was covered by the vaccine. The research is an important finding that helps researchers refine plans for future flu seasons. However, the authors themselves make some caveats that the reporting on this topic has overlooked.

The first is that the number of cases were so small that the confidence intervals were very large and went all the way down to 0. Because of this, the authors caution that their findings may not apply to other geographical locations. Another issue is that the number of hospitalizations were too low to estimate how well the vaccine reduced the number of hospitalizations. This was not discussed in the article when the vaccine was discussed. Even if the vaccine looses the ability to prevent infection later in the season, that protection still appears to be intact. 
Another issue is that the loss of effectiveness was only seen in those older than 65. Those younger than 65 had a rate of vaccine effectiveness that was similar to other locations. The issue of vaccination in those older than 65 is a well known problem that isn't limited to the flu vaccine. This could be solved through the use of adjuvants or possibly boosters part way through the season. But probably the biggest issue is the timing of the reporting of this article. If this had come out in July, it would be one thing. However, it got picked up by news sources in mid-September, right when people should start looking to vaccinate for the flu. Compounding problems, this article will probably get shared into December and may make some people delay vaccinating far too long. This is irresponsible journalism and bad science reporting. I'm working on a blog about this topic, but accuracy is crucial for science reporting as a bad report can cause great harm (such as causing people to delay getting a valuable vaccine when the time for delay has already passed).

This article is correct in one aspect though. There really isn't a need to get vaccinated for the flu in July or August if you are in the Northern Hemisphere. It could have better addressed this rather than make it sound like the vaccine loses effectiveness for everyone and not just the elderly (or at least has been observed in an atypical season). Late September and October are still good times to get the vaccine, unless there is no other choice. It's better to get this vaccine early than it is to delay getting it too long and risk infection before an immune response from the vaccine can develop. There are a lot of factors that go into this and it's not nearly as black and white as the reporting on this article make it seem. 

Saturday, September 24, 2016

Not another "zombie" virus (it's nothing to be scared of unless you are an amoeba)

Imaging of Mollivirus particles. (A) Scanning electron microscopy of two isolated particles showing the apex structure. (B) Transmission electron microscopy (TEM) imaging of an ultrathin section of an open particle after fusion of its internal lipid membrane with that of a phagosome. (C) Enlarged view of the viral tegument of a Mollivirus particle highlighting the layer made of a mesh of fibrils (black arrow), resembling Pandoraviruses’ intermediate layer, and the underneath internal membrane (white arrow). Three ∼25-nm interspaced rings are visible around the mature particle. (D) Light microscopy (Nomarski optics 63×) imaging of a lawn of Mollivirus particles, some of them (black arrow) exhibiting a depression at the apex. Figure via Legendre et al., 2016.

new study details the discovery of another giant DNA virus found in the Siberian permafrost. The new virus, called Mollivirus, is similar to another giant DNA virus that was also discovered in the permafrost, Pithovirus. However, although the pithovirus is oblong, the mollivirus is more round. It is also similar is structure to pandoraviruses, another set of large DNA virus. The mollivirus is smaller than some of the other large DNA viruses at 500-600 nm in diamter; however, it is still large enough to be seen with a light microscope (as seen by panel D in the picture above). Like the pithovirus, the researchers were able to infect an amoeba with the mollivirus and revive it. The genome is 651 kb long encoding for 523 proteins; 16% of the genes have their nearest orthologs to genes from pandoravirus and 10% to Acanthamoeba castellanii, most likely through horizontal gene transfer. As with these other large DNA viruses, most of the genes have no known orthologs. One of the more surprising findings is that ribosomes from the host are packaged into the virions. 

These large DNA viruses have changed the way we think about viruses. With genome sizes in these viruses ranging from 0.6 to 2.8 Mb, they are comparable in size to the smallest eukaryote parasites. Theses viruses have diverse morphologies as seen below. 


A Pithovirus. Credit: ulia Bartoli & Chantal Abergel; Information Génomique et Structurale, CNRS-AMU via Nature.

Marseillevirus at different stages of its formation in an amoeba.
Credit: Copyright Raoult / URMITE via Science Daily.

The complex interior of a Mimivirus. Electron microscopy at magnification of about 200.Credit: Didier Raoult, picture by N. Aldrovandi via Live Science.

Megavirus virion via Virology Blog.

Pandoravirus virion via Virology Blog.

Hopefully the reporting on the discovery of the mollivirus will be better than that of the pithovirus. When the pithovirus sample from Siberia was revived in amoebas, many science news sites proclaimed the scientists had resurrected a zombie virus and that unknown dangers lay in wait. The headlines from other news sources were much worse and I won't bother linking to them. Some news reports were much better and specifically mentioned that this virus posed no risk to humans. These viruses pose a risk to some organisms, but if you aren't an amoeba, then you'll be fine. These discoveries are offering vital clues into the evolution of viruses. Their discovery has also helped restart a conversation of if viruses are alive or not and what the definition of life should be.