Robot Contact Rate Activity for K-12 Students to do at Home

Since schools have closed across the country and world, parents and teachers are looking for learning activities that students can do at home. So I’m posting an easy experiment for Grades 3-6 that uses HEXBUGs, popular robot toys, to explore why we’re doing social distancing during the coronavirus pandemic. This activity could be modified for other grade levels. For instance, you could add in more replicates of each “treatment group” (number of robots), and then have students calculate and plot the means of each treatment group. Or you could have them use a line to predict how many contacts would occur for 10 or 20 robots—more than they probably own. Have fun!

ContactRateLab_K-12 <-PDF link

RobotContactRateLab

 

Bat Conservation and COVID-19

In the past week, my social media feeds – which encompass many people who love bats and support conservation – have been increasingly full of pleas and demands for the media to stop villainizing bats for the 2019-nCov outbreak. I can understand this sentiment; I certainly do not want mobs of people with torches and pitchforks to go out and cull bat colonies to try to protect human health. In fact, even in cases where the transmission of a deadly virus to people is ongoing, like transmission of rabies from vampire bats to people in Peru, killing a bunch of bats doesn’t necessarily reduce human risk; it might even increase it, due to complex disease dynamics! So the sentiment to be careful with how we portray the threats that bat-borne viruses pose for public health in news articles is one that I can support.

HOWEVER, today these social media posts contain a new element: a blog post by a famous bat conservation biologist, Merlin Tuttle, who argues that we have no reason to implicate bats in the 2019-nCov outbreak, and that researchers who are trying to find this virus and other viruses in bats are just in it for the easy research and grant money, because virus spillover from bats to people is very rare and not worth studying:

“…Compared to snakes or other animals, they [bats] are by far the easiest to quickly capture and process, have few defenders, and are already widely feared. Associating bats with rare, little-known viruses provides tempting opportunities for quick publication, big grants, and career advancement14.

Nevertheless, history does not support this bias. The great pandemics have come from birds, rodents or primates, not bats15. In truth, bats have one of our planet’s finest records of living safely with humans2,14.”

If you have been a long-term follower of this blog, you’ll know that I have never once criticized a paper or focused on the negatives, because I generally find that to be unproductive. But this is not Merlin’s first wildly irresponsible post that pits the general public against researchers by misrepresenting the scientific literature, and I fear that this one could have real negative impacts. So in this space, I want to provide some resources to people interested in bat conservation to learn more about how viral spillover events (like this coronavirus epidemic) and bat conservation are related.

Let’s start with some general information about spillover of viruses from bats. There is no question that bats are reservoirs for many viruses that cause serious human illnesses.  These include viruses like SARS, rabies, and some paramyxoviruses like the Hendra and Nipah viruses.  Because these viruses are such a big deal, there has been a lot of recent attention to bats and their potential as reservoirs for high-impact emerging zoonotic viruses. This work has shown that bat species do seem to be reservoirs for a disproportionate number of viruses, on average, in comparison to species in other taxonomic groups, like rodents. And there might be several reasons why bats have so many viruses but can live with them without being sick. Bats are reservoirs for many coronaviruses and similar viruses (e.g., SARS), so it is highly like that the 2019-nCov has a bat reservoir.

Bats can infect people with these viruses in many different ways. For instance, people can become infected by the rabies virus when they are bitten by a bat or when they contact bodily fluids from bats. People could also become infected by batborne viruses by handling bats or consuming bats, or by consuming things that bats defecated on/in (as in the palm sap and Nipah example). And finally, bats can infect other wildlife or domesticated species, and people can become infected by contacting/consuming those other species. We do not know which transmission route led to spillover from bats to people for this coronavirus, but in general, wildlife markets (for consumption or pet trade) do bring together bats, other wildlife, and people in unnatural ways, and there is a lot of potential for spillover from bats to people in these settings.

Viral spillover from bats is a real threat to global human health and has serious impacts on global economies, so we should be doing everything we can to neutralize those threats. One of the best ways to do that is by advancing global bat conservation. In particular, if we can keep bats in their undisturbed, natural habitats, we can minimize the chances of bat to human transmission. This isn’t as easy as saying, “Stop eating bats!” The global community needs to make a real effort to ensure that in places with high bat diversity (and thus high bat virus diversity), people are empowered to conserve bat habitats and bats because they have enough to eat, don’t need to cut down forests for fuel, etc.

If you have helpful resources for learning more about spillover of viruses from bats and how to use these spillover events as opportunities to advance local and global support for bat conservation, please leave them in the comments!

Contact function lab for undergraduate or graduate courses

Hello, Educators! Contact rate functions are a central component in SIR models, but they can be difficult to cover in disease ecology courses, because things get “mathy”. So I developed a hands-on contact function lab that allows students to discover and explore the various contact functions using experiments with tiny robots, called HEXBUGs. HEXBUGs are so fun to use that other people have developed similar labs, and I borrowed the awesome SkyNet premise from one such lab designed by David Civitello. If you want to adapt and run a lab like this, you can buy the HEXBUGs online or in a toy store near you. I’m sharing the worksheet that that I used for this lab, which you are welcome to edit and share as you please. I’m also happy to send you the answer key and the final graph to help pick the best HEXBUG densities to use in your lab. Happy educating!

Lab Worksheet (Word doc)

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IMG_20190916_122519976

Extreme competence and extreme incompetence

The February reading group paper was “Extreme Competence: Keystone Hosts of Infections”. If you’ve been following the blog for awhile, you probably know that this is a topic near and dear to my heart; I’ve often mused about superspreaders, superreceivers (here and here), and other types of “super hosts”. In fact, I think about this so often that I’ve started to get a bit bored with wondering why some individuals in a host population or some host species are really good at passing on their parasites. As Martin et al. (2019) point out, the superspreader idea is pretty sexy and superspreaders might be especially conspicuous, so it seems like everyone is looking for them and talking about them. But not me. My new quest is to figure out what makes a host “bad”.

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In my hunt for bad boys (most of which cannot be discussed in a public venue), I worked on an idea that wasn’t brought up in the Martin et al. (2019) paper: other symbionts can make hosts super bad for parasites. That’s right, folks. Without a substantial Twitter discussion to guide this post, y’all are being subjected to a story from my dissertation. BRACE YOURSELVES.

On almost every continent on this planet, there are freshwater snails, and it seems like all of those snail species are at least sometimes infested by little ectosymbiotic oligochaete worms, called Chaetogaster limnaei. Chaetogaster are fascinating for several reasons, but their claim to fame in the literature is their diet: they’ll eat anything that fits in their mouths, including trematode parasites. From a snail’s perspective, this is awesome, because they gain at least some protection from being infected by trematode eggs, miracidia, and cercariae. In fact, after an absolutely abhorrent amount of pipetting – which caused by left thumb to grow a muscle as big as an egg – I found that the more Chaetogaster a snail had, the less likely the snail was to get infected by free-swimming trematode larvae. (And because Chaetogaster rapidly asexually reproduce, the more free-swimming trematode larvae a snail is exposed to, the more Chaetogaster it suddenly has, meaning that snails in risky waters get increased parasite defenses!)

Snails with many Chaetogaster are not a good target for trematodes, in the same way that a hotdog stand surrounded by hungry lions isn’t a good target restaurant for buying your lunch. But this probably isn’t particularly inconvenient for trematodes, because just just like most hotdog stands aren’t surrounded by hungry lions, most snails don’t have many Chaetogaster. As I’ve blogged about before, Chaetogaster are aggregately distributed amongst snail hosts, such that most snails have 0 or 1 worms, and just a few snails have many worms. Therefore, just a few snails are what we might call “super bad hosts”.

Screen Shot 2019-03-04 at 9.55.55 AM

As Martin et al. (2019) point out, we know that 20% of hosts are typically responsible for 80% of parasite transmission. That 20% contains the superspreaders that we’re all so excited about. But my dissertation work shows something else: ~20% of hosts are “super bad hosts” that might be acting as superdiluters, with Chaetogaster literally sucking up the trematode population. This is interesting because Chaetogaster is just one defensive symbiont species in a world full of hosts covered in symbionts that eat parasites. Defensive symbionts are probably affecting host competence in many, many systems, so these interactions might be a good place to look as we start carefully quantifying variation in host competence within populations.

Finally, since we’re talking about symbiosis today, I’ll leave you with some advice: this year’s March Mammal Madness has an ENTIRE LINEUP of symbioses, including ants + aphids and Bornean bats + pitcher plants. Obviously, one of these will be the 2019 champion. Go fill out your brackets accordingly!

February Reading Group Paper: Extreme Competence

Happy Friday, Everyone!

It’s time for our second monthly paper for the 2019 Parasite Ecology Reading Group! I’m going to lead this second paper, and the paper I picked is:

Martin LB, Addison B, Bean AGD, et al (2019) Extreme Competence: Keystone Hosts of Infections. Trends in Ecology & Evolution. doi: 10.1016/j.tree.2018.12.009

Last month, I wasn’t speedy in my replies to Twitter comments, because I was working from two accounts. I should be more responsive this month! Give the paper a read and share your comments/questions/cartoons in the comments section on this post or on Twitter. I’ll incorporate them into my post at the end of the month.

Please remember our Rules of Engagement:

  • DO ask questions if you do not understand some aspect of the paper.
  • DO say nice things about the paper: tell us why you think the results are important, wax eloquent on your favorite figure, etc.
  • DO share your cartoons/scribbles, puns, poems, etc. that were inspired by the paper. As long as they’re respectful and PG-13, I’ll post all of them!
  • DO pick papers that everyone will enjoy and/or benefit from reading, which is especially likely if you pick readable papers from relatively high impact journals.
  • DO respectfully engage with the rest of the community; help us answer questions and have lively discussions!
  • DO NOT criticize the papers, even if you do it “in a nice way”. I will delete any blog comments that negatively assess any aspect of any paper (study design, stats, conclusions, etc.). I don’t have the power to delete your Twitter comments, but I will ask you to stop participating. You are welcome to share your critical thoughts elsewhere, but this blog is not a venue for bashing peer-reviewed literature.

What is a neglected tropical disease?

When I first sat down to write this post, I thought that I’d start with a quick definition of the term Neglected Tropical Disease (NTD). I thought I knew what an NTD was – I even study a few! – so I was surprised when a definition didn’t immediately pop into my head. And I wasn’t alone. Several people who read our January Parasite Ecology Reading Group Paper also wondered how we decide which human infectious diseases should be considered NTDs.

If you’re like us, you probably thought about Googling it; surely WHO, CDC, etc. have some sort of NTD definition? They sort of do. But while major health organizations all use generally similar verbiage on their websites and in their reports, none of them seem to have a particularly precise definition. It would be hard to use their definitions to decide whether a given human infectious disease was an NTD or not.

What we seem to have instead of a precise definition is the World Health Organization’s list of 18 NTDs. And what an ecologically interesting list it is! There are viruses, bacteria, protozoa, and helminths. There are parasites with vectorborne transmission, fecal-oral transmission, and environmental transmission. Such diversity! In fact, at first glance, the NTDs seem to have little in common. And at second glance, the list seems oddly short. For instance, this article shared by Valentin Greigert asks why hepatitis E, which kills 70,000 pregnant women a year, doesn’t make the list.

The crux of the issue seems to be deciding who is neglecting NTDs. Is it politicians? Is it researchers? Funding agencies? Drug developers? Rich nations? This is a difficult question to answer, because it requires quantifying how much attention different human infectious diseases are receiving.

To figure out which diseases are or are not neglected by research, Furuse (2018) counted the number of publications (i.e., one metric of research effort) for 52 human infectious diseases, to see if NTDs are studied less than non-NTDs. They found that relative to their disease burdens, only a few NTDs are understudied. The only NTDs that were considered understudied relative to their global burdens were lymphatic filariasis, trichuriasis, ascariasis, onchocerciasis, hookworm disease, and trematodiasis. And, as the above article suggested would be the case, some diseases that are not on the accepted list of 18 NTDs had relatively high burdens and relatively few published studies, like paratyphoid fever. (To see the full list, go check out the paper.)

Over on Twitter, there was some interesting discussion about why some diseases had relatively many or few research papers relative to their burdens. In general, it was hard to guess, and Furuse (2018) notes that the reasons are potentially unique to each disease. And thus our conversation kept circling back to whether and how this burden-adjusted research intensity method could be useful in identifying and controlling NTDs. My personal ponderings have been about which types of research papers could be most indicative of neglect vs. attention. For instance, many NTDs already have effective and relatively cheap control methods that are sufficiently deployed in rich nations but not in poor nations, like water sanitation, so we might not need much research on ways to interrupt transmission for those NTDs. Instead, we might need research on where/when those controllable NTDs exist or the best ways to deploy control operations. And thus only some types of research are highly relevant for any given NTD? Anyways, there is a lot to ponder about this neat analysis. You should give it a read and share your thoughts with us!

In closing, I’ll leave you with this description – not a definition – of NTDs. Maybe one day I’ll be able to amend this post with a precise definition. 

Neglected Tropical Diseases…

…are diseases that affect poor populations that lack basic requirements like clean water, sanitation, education opportunities, and access to affordable healthcare. If you don’t study infectious diseases and you aren’t poor, you probably haven’t heard of more than four of the 18 NTDs in the figure below, despite the fact that they affect billions of people.

…trap people in a disease–poverty cycle. No matter how hard they work or how much economic assistance they receive, populations afflicted by NTDs will remain impoverished without disease control efforts because their disease burdens continue to result in lost economic mobility.

…disproportionally affect tropical and subtropical nations because poverty (i.e., people making less than $1 USD per day) is prevalent in “the global south”. But NTDs aren’t restricted to the the tropics. For instance, it is difficult to estimate NTD burdens, but NTDs are thought to affect thousands to millions of people in the United States.

…tend to be chronic diseases that cause substantial human morbidity, rather than mortality, but several of NTDs do cause substantial mortality, especially in children.

…can often be prevented/controlled/treated using existing, effective, and relatively cheap methods, such as education and water sanitation, but not always. When control methods are lacking, NTDs are often neglected by drug research and development efforts, because it isn’t usually profitable to develop drugs for people who won’t be able to pay for them.

…lack public and political visibility and discourse because they affect people with limited economic and political power, they are associated with stigma/shame, and/or they don’t have high, news-worthy mortality rates like HIV/AIDs, tuberculosis, and malaria.

Figure taken from here:

NTD fig

January Reading Group Paper: NTDs vs. Research Effort

Happy Friday, Everyone!

As promised, I am posting our first monthly paper for the 2019 Parasite Ecology Reading Group! I’m going to lead this first paper, and the paper I picked is:

Furuse Y. Analysis of research intensity on infectious disease by disease burden reveals which infectious diseases are neglected by researchers. Proc Natl Acad Sci USA. 2018; 201814484. doi:10.1073/pnas.1814484116

I was able to see the full text in HTML format by clicking “View Full Text”, so hopefully everyone has access, regardless of library affiliation.

Give the paper a read and share your comments/questions/cartoons in the comments section on this post or on Twitter! I’ll incorporate them into my post at the end of the month.

Please remember our Rules of Engagement:

  • DO ask questions if you do not understand some aspect of the paper.
  • DO say nice things about the paper: tell us why you think the results are important, wax eloquent on your favorite figure, etc.
  • DO share your cartoons/scribbles, puns, poems, etc. that were inspired by the paper. As long as they’re respectful and PG-13, I’ll post all of them!
  • DO pick papers that everyone will enjoy and/or benefit from reading, which is especially likely if you pick readable papers from relatively high impact journals.
  • DO respectfully engage with the rest of the community; help us answer questions and have lively discussions!
  • DO NOT criticize the papers, even if you do it “in a nice way”. I will delete any blog comments that negatively assess any aspect of any paper (study design, stats, conclusions, etc.). I don’t have the power to delete your Twitter comments, but I will ask you to stop participating. You are welcome to share your critical thoughts elsewhere, but this blog is not a venue for bashing peer-reviewed literature.