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 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.