Bot Flies in Squirrels: What to Do – A Quick Guide for Worried Wildlife Enthusiasts

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Bot flies are a group of parasitic insects that lay their eggs on various mammals, including squirrels.

The tree squirrel bot fly, or Cuterebra emasculator, is a species native to the Americas and can be found in places like Florida.

These parasites can cause harm to their hosts, leading to discomfort, infection, and, in some cases, death.

Bot Flies in Squirrels
Rabbit Bot Fly

Knowing how to prevent and treat bot fly infestations in squirrels can help protect these creatures and maintain a balanced ecosystem.

Some ways to address this issue include hygiene, habitat maintenance, and chemical treatments.

It’s important to monitor squirrel populations for signs of infestation and intervene when needed.

Understanding Bot Flies in Squirrels

Bot Fly Life Cycle

Bot flies have a unique life cycle. Adult bot flies do not feed or take in nutrients, and they show a high degree of host specificity1.

Their larvae parasitize rodents like squirrels, and their development depends on the specific host they infect2.

Rodent Bot Fly Maggot

Squirrel Bot Fly Species

The tree squirrel bot fly is one example of a Cuterebra species.

There are around 30 Cuterebra species native to the Americas3. Five of these species are found in Florida2.

Common Hosts

Cuterebra larvae typically parasitize native rodents (e.g., mice, rats, tree squirrels) or lagomorphs (e.g., rabbits, hares)2. The host can influence the development of the bot fly.

  • Tree squirrels
  • Rats
  • Mice
  • Rabbits
  • Hares

If an animal like a cat consumes one of these hosts, it too, can become infected

Comparison Table: Cuterebra Species & Hosts

Cuterebra Species Preferred Hosts
C. emasculator Tree squirrels
C. fontinella Mice, rats
C. cuniculi Rabbits, hares

Symptoms and Effects of Infestation

Warbles and Skin Lesions

Infestation of squirrels by the bot fly larvae, known as Cuterebra emasculator, can lead to the appearance of warbles, which are bulges formed under the skin.

These warbles often have a small hole in the center for the larva’s breathing tubes to extrude through.

Skin lesions may also occur during infestation, causing hair loss and dark, thickened skin.

Tumors and Lumps

In some cases, the bot fly larvae may cause the formation of tumors or lumps as they parasitize inside the squirrel’s body.

These lumps can be mistaken for other diseases or conditions.

Rodent Bot Fly

Comparison table between bot fly infestation and other diseases:

Condition Appearance Cause
Bot fly infestation Warbles, lumps; sometimes accompanied by skin lesions Cuterebra emasculator larva
Squirrel pox Skin lesions, pustules, and scabs Squirrel pox virus
Notoedric mange Hair loss, dry and thickened skin without crust formation Notoedric mite

Effects on Squirrel Health

Though bot fly infestations can be unsightly and uncomfortable for squirrels, most healthy adult squirrels can recover from the infestation without long-term effects.

However, in some cases, it may lead to secondary infections, illness, or even death, especially in weaker or younger squirrels.

Identifying and Treating Infested Squirrels

Assessing the Infestation

When assessing a potential bot fly infestation in squirrels, look for signs such as:

  • Swelling or lumps on the squirrel’s body
  • Restlessness or discomfort
  • Hair loss around the affected area

Bot fly infestations are typically caused by the tree squirrel bot fly (Cuterebra emasculator).

The female bot fly lays eggs near the squirrel’s habitat, and the larvae burrow into the squirrel’s skin, causing wounds.

Rodent Bot Fly

Consulting a Veterinarian or Wildlife Rehabilitator

If you’ve identified a bot fly infestation in a squirrel, it’s essential to consult with a veterinarian or wildlife rehabilitator for advice. They can:

  • Assess the severity of the infestation
  • Recommend appropriate treatment options
  • Provide guidance on preventing future infestations

Treatment Methods

There are several methods for treating bot fly infestations in squirrels. Some common treatment options include:

  • Manual removal: The larvae can be carefully extracted from the squirrel’s skin by a professional. However, this can be risky and may potentially harm the animal.
  • Medication: In some cases, medication may be prescribed to help the squirrel’s body naturally expel the larvae.
  • Supportive care: Providing the squirrel with a safe, clean environment and proper nutrition can help its body recover from the infestation.

It is crucial to remember that treating bot fly infestations should be done by a professional to ensure the safety and well-being of the squirrel.

Prevention and Control

Environmental Modifications

One way to prevent and control bot flies in squirrels is to modify their habitat.

By cleaning up vegetation, like overgrown bushes and tall grass, you can reduce nesting sites for rodents and lagomorphs, which are the main hosts of bot flies.

Some examples of animals that could be hosts include rabbits, hares, chipmunks, and tree squirrels.

Additionally, managing the populations of predators such as foxes, wolves, and deer can naturally help control the number of potential hosts.

Rodent Bot Fly

Protecting Pets and Other Animals

It’s essential to protect your pets and other domestic animals from bot fly infestations.

For instance, dogs and cats should be kept away from areas with high rodent populations or where bot flies might be prevalent.

Moreover, regularly checking your pets for signs of infestation, such as skin lesions or lumps, can help in early detection and treatment.

In case of infestation, consult your veterinarian for appropriate treatment options.

Human Interaction and Risks

Potential for Human Infestation

Bot flies, such as the tree squirrel bot fly, mainly infest rodents and lagomorphs (rabbits and hares).

There is a low risk of human infestation as bot flies are host-specific, and the species affecting squirrels do not naturally infest humans.

Squirrel Consumption Safety Tips

If you plan to hunt and consume squirrels, consider the following safety tips:

  • Inspect for bot fly larvae: Check the squirrel’s skin for signs of infestation, such as bumps or irritated open wounds.
  • Skin and clean the animal: Properly skin and clean the squirrel, removing any bot fly larvae found.
  • Cook the meat thoroughly: Ensure the meat is cooked completely to prevent possible transmission of pathogens from larvae.

Minimizing Encounters with Infested Squirrels

To reduce the chances of coming across squirrels infested with bot flies, consider the following:

  • Check local populations: Be aware of the presence of bot flies and infested squirrels in your region.
  • Limit close contact: Avoid directly handling squirrels, especially if you notice signs of infestation.

By following these guidelines, both hunters and individuals can minimize the risks associated with bot fly-infested squirrels.

Remember to practice proper hygiene and safety measures when interacting with wildlife.


Bot flies, particularly the Cuterebra emasculator species, pose a threat to squirrels across the Americas.

While these parasitic insects are host-specific, their infestation can lead to discomfort and potential health risks for the affected squirrels.

Wildlife enthusiasts should be aware of the signs of bot fly infestation and take preventive measures, such as habitat maintenance and monitoring squirrel populations.

If an infestation is suspected, prompt consultation with a veterinarian or wildlife rehabilitator is crucial. By understanding and addressing this issue, we can ensure the well-being of our squirrel populations.


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Reader Emails

Over the years, our website, has received hundreds of letters and some interesting images asking us about bot flies. Scroll down to have a look at some of them.

Letter 1 – Bot Fly

Giant Fly
Location: Yakima, WA
November 1, 2010 4:18 pm
Biggest dipteran I’ve ever seen.
Signature: Paul Huffman, President-for-Life, Moclips Surf Club

Bot Fly

Hi Paul,
We strongly believed that you had submitted an image of a Bot Fly in the family Oestridae, but most individuals we have identified in the past are marked with black and white patches similar to the patterns on a Holstein milk cow

We quickly found a matching photo on BugGuide that is identified as the Bot Fly Cuterebra tenebrosa, and Natalie McNear from Marin County California who submitted the photo wrote:  “Looking on here it most closely resembles the New World skin bot flies of the subfamily Cuterebrinae, but I don’t see any on here that are all dark with a metallic blue abdomen.” 

There is a comment by Jeff Boettner on the posting that indicates:  “I am pretty confident this one is likely Cuterebra tenebrosa. There are a few other species that have all black females, but you have shots from all angles, so likely this is correct. The bot uses Neotoma (wood rats) as a host. … There is a very robust comment dialog on that posting that is well worth the time to read. 

The genus information page on BugGuide provides this information on the life cycle of the Bot Flies:  “Females typically deposit eggs in the burrows and ‘runs’ of rodent or rabbit hosts. A warm body passing by the eggs causes them to hatch almost instantly and the larvae glom onto the host. The larvae are subcutaneous (under the skin) parasites of the host. Their presence is easily detected as a tumor-like bulge, often in the throat or neck or flanks of the host.

The larvae breathe by everting the anal spiracles out a hole (so they are oriented head-down inside the host). They feed on the flesh of the host, but only rarely does the host die as a result. Bot Flies are also known as Warble Flies. These Bot Flies really are quite large and they resemble bumble bees in both appearance and sound.

Bot Fly

Letter 2 – Bot Fly

Subject: Weird, weird fly in Wisconsin.
Location: Wisconsin, USA
June 25, 2012 3:24 pm
Hi there,
Do you have any idea what the heck this is? I found it in my window — it’s about 1” long, very hefty. Apparently dipteran. This creature has a weird thing sticking out of the front of its head (mouthparts? emerging parasite?) and a couple of black upright ”fins” on its back just forward of the wing bases.
I’m an amateur entomologist and I’ve never seen the likes of this blighter before.
Thanks, and I’m interested in what you come up with!
Best wishes,
Signature: Rhian

Bot Fly

Dear Rhian,
This is some species of Rodent Bot Fly in the genus
Cuterebra.  Bot Flies are parasitic flies.  BugGuideprovides this graphic description of their life cycle:  “Females typically deposit eggs in the burrows and “runs” of rodent or rabbit hosts.

A warm body passing by the eggs causes them to hatch almost instantly and the larvae glom onto the host. The larvae are subcutaneous (under the skin) parasites of the host. Their presence is easily detected as a tumor-like bulge, often in the throat or neck or flanks of the host.

The larvae breathe by everting the anal spiracles out a hole (so they are oriented head-down inside the host). They feed on the flesh of the host, but only rarely does the host die as a result.”  We are copying Jeff Boettner to see if he is able to provide a species identification for us.

Bot Fly

Dear Daniel,
Thanks very much for the I.D. on that peculiar creature! The pictures in the link you sent look exactly like it, right down to the “fins” on the back (which I suppose are some kind of halteres?).

That’s certainly a bizarre life cycle for a strange looking creature; for some reason, I thought bot flies were mostly tropical.
Thanks again, and keep up the good work with the site! 🙂
Best wishes,

Jeff Boetner replies
Hi Daniel and Rhian,
Great shots. Yes, a Cuterebra botfly, this is one of the Cuterebra fontinella bots. You have two subspecies of this bot in WI, Cuterebra fontinella fontinella, which uses white footed mice as a host, and Cuterebra fontinella grisea, which uses deer mice as a host.

The one you photographed is very freshly emerged, the wierd face is from a balloon like structure that inflates to help push the fly out of the pupal case, and then it gets reabsorbed back into the face. These guys don’t feed as adults so have no real mouth parts.

It is hard for me to do this one to species, but if you hung onto it, it might get better coloring after it has been alive for a few days. So if you can keep it alive, (they don’t feed so easy to keep), post another picture once the brown turns to white and black. I don’t see these this fresh, very often, unless I have reared one. Very fun to see.

I am doing dna work on bots, and I would be interested in the specimen. I don’t have dna from WI specimens, and still missing grisea if it turns out to be that one? Yours is female for sure from the spacing between the eyes.
Thanks for posting. And thanks for the forward Daniel. Love you site!
Jeff Boettner
Plant, Soil and Insect Sciences

Letter 3 – Bot Fly

Hey Bugman,
Love your site and use it a lot. I believe this is a new born
Carpenter bee. I watched and listened to a Queen bore a nest in the railing of my deck this spring.

This morning I found this on a leaf below where the hole from the nest is. I thought I would share with you and your followers these pictures of a new born. It has quite a “cute” pig like face and exclamation points in it’s eyes. Thank you,
Chicago, Illinois

Hi Glenn,
You are mistaken in your identification. This is not a bee, but a fly. It is a Bot Fly to be exact. Bot Flies are mammalian endoparasites.

There are species in the tropics whose larvae live inside human hosts, but the North American species are parasitic on rodents. They are also called Warble Flies. Eric Eaton has this to add: “Hi, Daniel: The bot fly is another species in the genus Cuterebra, the rabbit and rodent bot flies.

The red in the eyes is characteristic of some species. Don’t know if there is a good website on them, but there is a great technical book on them with some nice images and lots of information on their bizarre biology…. Eric”

Letter 4 – Bot Fly

Looks like a bumblebee with a fly bottom?
Location: Petawawa, Ontario
June 8, 2011 10:36 pm
When I found this lovely critter beside my pool, I thought it must be a half-drowned bumblebee as it’s about the same size and shape as a bumblebee. I poked it gently with a stick to see if it was alive,and it squirted something out of it’s rear end in a stream of what I figured was some sort of venom.

(It got some distance with the spray, too, about 12 inches in a fine arc onto my lawn!)
I quickly got a bottle (and lid) from the house to carefully capture it and get a better look. It didn’t seem to have a mouth or a stinger, and had a fuzzy head but shiny bottom like a fly.

Also, I noticed it didn’t have the same kind of wings as a bee. After I did some online searching and overcame the heebee jeebees, we got some clearer pics, this hefty fella was flushed down the toilet… just to be safe.
After you correctly identified our Luna Moth visitor, I knew exactly where to go for an answer on this one.

Am I close with my guess that this is some type of botfly? It doesn’t have the red stripes on it’s eyes that I’ve seen from some other images, but the shape of the body and other features look familiar.
Signature: Anderson Family

Bot Fly

Dear Anderson Family,
We will leave the species identification to the experts, but you are absolutely correct in your guess that this is a Bot Fly in the genus
Cuterebra.  Of the species on bugGuide, out best guess would be Cuterebra emasculator, and there is a comment posted that includes this information: 

“This is our only golden haired bot in the Northeast and this species can be found anywhere east of the Mississippi although rarely seen. It is primarily host specific in the Northeast on chipmunks, Tamias striatus.”

Letter 5 – Rabbit Bot Fly

Subject: Giant Fly
Location: Denver, Colorado
July 7, 2012 12:21 pm
Found this thing outside on the patio, it’s wings were incredibly small/shriveled when we found it, but have grown a lot by now. What in the world is it?! Looks like some kind of giant fly…but could it be a horse fly? The eyes aren’t together so it doesn’t seem like it. Thanks!
Signature: Thanks!

Newly Metamorposed Rabbit Bot Fly

Your insect is a freshly metamorphosed Bot Fly in the genus Cuterebra.  Both the wrinkled wings and the protrusion on the face indicate the recent eclosion.  Jeff Boettner provided this information for a recent posting:  “The one you photographed is very freshly emerged, the wierd face is from a balloon like structure that inflates to help push the fly out of the pupal case, and then it gets reabsorbed back into the face.”  We will copy Jeff on this response to see if he is able to provide any additional information.

Jeff Boettner responds
Hi Daniel and Tyler,
Your bot looks like Cuterebra lepusculi, a rabbit botfly. They are a little tricky to ID until they have been alive for a day or two, yours is freshly emerged.

If you keep it around for a few days the face will be helpful to see as well as the pattern on the hind end. Bots do not feed as adults, so are easy to hang onto them, although they only live for about 10 days. Their goal is to find a mate and then infect rabbits.

I am doing dna work on reworking the botflies, and would love to get this as a specimen, if you are willing to part with it? We are working on a National Science Foundation grant proposal, and rabbit bots are difficult to get. I would put the specimen in the Smithsonian collection when I am done with it. We use part of one leg for dna work, which we fresh freeze to -80C until we do the sequencing.

We hope to look at the evolution of botflies and their hosts. This work will also go toward making a better field key to better help identify bots.
I am happy to cover your shipping costs. Can be shipped live or dead in a pill bottle, if dead add some tissue to bottom and top to prevent bot from moving a lot in shipment.
My address
Jeff Boettner
Plant, Soil and Insect Sciences
Room 115 Ag. Eng. Bld.
250 Natural Resources Road
Amherst, MA 01003

Nice post. Daniel does a great job with whatsthatbug! I learn a lot from the site. Keep up the great work.

Update from Jeff Boettner
July 17, 2012
Hi Tyler (cc’ing Daniel)
Just to let you know the bot arrived in excellent condition. It is a female Cuterebra lepusculi for sure, which is a rabbit bot. It uses cottontail rabbits as a host, (mostly Sylvilagus audubonii and Sylvilagus nuttallii as hosts in your area).
Thanks so much for sharing it.

I will freeze a leg and use it for our next dna run. A tough one for me to find. Will add the bot to our collection which will head to the Smithsonian collection eventually.

Tyler I will drop a check to you to cover your postage and time.
Daniel, I just did a donation to whatsthatbug too, for calling this (and other bots) to my attention. A huge help for our study. Keep up the great web site.
Thanks to you both. Keep on hunting and id’ing

Note: They just killed off our Plant, Soil and Insect Sciences Dept. So I am now officially in Dept. of Environmental Conservation. We HAD the oldest Ent Dept in the country. Otherwise I have the same address and email for now.
Jeff Boettner
Dept of Environmental Conservation

Hi Jeff,
We are horrified to learn that the oldest entomology department in the country is now defunct, and it doesn’t seem like a timely move since there appears to be more and more interest in insects since we began writing this online column back in 1999 on the now defunct American Homebody website after the zine American Homebody went online. 

That was very kind of you to make a donation to WTB?  We will continue to notify you whenever a Bot Fly is submitted for posting or identification.  What is the peak season for Bot Flies.  We can make a nice featured posting at that time recommending people to send you specimens or at least to contact you.

Another Update from Jeff
Hi Daniel,
Bots are very random and hard to predict. Generally the bulk of bot reports come in starting with some western bots in April to bots from all over in July-August, then back to western bots in Sept-Oct. So I think it would be hard to time a write up.

Luckily these guys are big so they tend to draw attention. And rabbit bots with their red eyes tend to get over reported, in spite of the fact that- in the wild- they are quite hard to find. So really neat to see what turns up on your site and BugGuide.

Between the two of you, I have seen about 1/3 of all the bots show up, including the really rare C. mirabilis ( the male has still never been seen, and the female on BugGuide is only the 3rd specimen known in the world), and C. bajensis (which I got a specimen via BugGuide) and only known from about 15 specimens in the world. I got a specimen and dna from the second one, the first one above I flew out to New Mexico to talk to the family that found it –it had been buried in their yard by their kid- with a flower funeral- I would have put it in the Smithsonian :).

We found the host rabbits in the area and I hope to work with a couple of rabbit biologists to try to find bots to rear out a male so it can be described in the near future. So I am having fun with even the random bots that show up.

I am thinking about doing a write up for American Entomologist telling about the value of both your site and BugGuide. I have had a ton of fun stories about doing this quest for bots. Last year I had an 8 year old post a male C. lepusculi (the same species of rabbit bot you just got me) from Texas.

He just started collecting insects and didn’t want to part with it. I negotiated a deal with his dad to get him some BioQuip equipment in exchange for the bot. A few days later a 7 year old found the female also in Texas. So I did the same deal.

Turned out the kids lived about 8 miles apart so I connected them so they could go collecting together. Fun. That bot is pretty tricky to find in the wild, I have never seen this species in the wild, but now have 3 for our work thanks to you guys.

We sequenced the dna from the first two bots from TX and this was used in part of a proposal we wrote to the National Science Foundation to try to get funding to do more extensive dna work.

We made the first cut, and now are trying to write a full proposal (due in August). It may take us a few years to pull off a working grant, but this would allow us to do 454 sequencing (which is current state of the art), but costs about $400 a fly to run. But each fly we can do will get us a bit closer to understanding both fly and mammal evolution. So cross your fingers!

So for now, this is working great for me. Bots are very hard to set out to look for them. Although I have thought about taking out an add in New Mexico newspapers (like a wanted poster) to try to have people watch for C. mirabilis in and around Albuquerque, NM during the middle two weeks of Sept.

All three known specimens showed up within about 30 miles of this area during that time. I have spent about 10 days hunting for it so far. Keeps me off the streets.
Thanks for your concern about the Dept. We will still have some entomologists shifting to the Stockbridge School of Agric (within UMASS).

But was a big surprise to all of us that they would break up PSIS. (they merged entomology and plant and soil sciences about a decade ago to try to save ent, but now have pretty much killed it off with this move). The current profs will stil be around, but the plan is to not rehire when this batch retires, and about 1/2 are already within a few years of retirement age. So not looking good.

I agree, it is crazy given we are seeing about 3 new insect species every year in Massachusetts alone. And soon no one to work on them. And meanwhile emerald ash borer is now about 30 miles from our MA border, and Sirex wood wasp is also in NY…crazy to name a few.

Letter 6 – Bot Fly

Subject: Is this a Bumble Bee?
Location: Central New Hampshire
July 20, 2013 4:28 pm
Black and white markings, about the size of a Bumble Bee. Have never seen a bee
quite like this. It was very near a DogWood Tree in our yard.
Signature: Psquare

Bot Fly
Bot Fly

Dear Psquare,
It is easy to mistake this Bot Fly for a Bumble Bee.  Bot Flies are true flies and they are parasitic in the larval form, and according to BugGuide:  “The larvae are subcutaneous (under the skin) parasites of the host.

Their presence is easily detected as a tumor-like bulge, often in the throat or neck or flanks of the host. The larvae breathe by everting the anal spiracles out a hole (so they are oriented head-down inside the host). They feed on the flesh of the host, but only rarely does the host die as a result.” 

We are going to copy Jeff Boettner in our response in the hope that he can identify the species of Bot Fly you have photographed.

Hi Daniel and Psquare,
Your bot fly is a Cuterebra fontinella fontinella bot. This bot is a parasite of white footed mice, Peromyscus leucopus. Its a little hard to see the key features (a side view is helpful) but there are only a handful of bots in NH and this is the most common bot in your area.

The other bots have either red eyes (rabbit bots) or more white or yellow on their backs. So I am confident of this ID. By the distance between the eyes, this one is a female.
Thanks for the post.
Jeff Boettner


  • Bugman

    Bugman aka Daniel Marlos has been identifying bugs since 1999. is his passion project and it has helped millions of readers identify the bug that has been bugging them for over two decades. You can reach out to him through our Contact Page.

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    Piyushi is a nature lover, blogger and traveler at heart. She lives in beautiful Canada with her family. Piyushi is an animal lover and loves to write about all creatures.

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8 Comments. Leave new

  • I have 3 bot flies that have taken up residence in my picnic table. It started a couple of years ago I noticed them flying around the table & in my garden feeding on the squash pollen. I took pictures as best I could. This year I discovered they had bored a hole in the bottom side of the table. It is made of clear heart redwood & the hole came up from underneath. It was about 1/2″ in dia. & extended abt. 8″ horizontally. 2 of the flies are black & 1 is golden. I have pictures if you can tell me how to send. Dean

  • equalrights4parasites
    October 18, 2011 2:52 pm

    Dear Andersons,
    You found a chipmunk botfly, Cuterebra emasculator. The bots name is unfair, they don’t really emasculate their host (as was thought when named). I believe yours is a female, although a bit hard to tell from the pic. It could have been shooting off eggs when hassled. They can lay up to a thousand eggs per female. I would have loved this specimen. I am working on these bots as we speak. In the north these bots use chipmunks mostly as a host, and in the south they use grey squirrels. So these may be two subspecies. I am trying to look at dna to compare northern and southern emasculator specimens. They do buzz like a bee when held, and do look much like a bee, but only have 2 wings-bees 4. Nice detective work, only the rabbit bots have red in the eyes. So good job keying it on your own.

    Jeff Boettner
    Plant, Soil and Insect Sciences
    Amherst, MA

  • equalrights4parasites
    October 18, 2011 2:57 pm

    Dear ColeDean,
    Bugman is correct. Yours are not bots, but carpenter bees. Bots do not have mouth parts and hence they don’t feed as adults, ie they can’t nectar. Bots also do not burrow into wood, but carpenter bees do. Bots do look a lot like them for sure, but bots only have 2 wings.

    Jeff Boettner

  • Antikythera
    July 4, 2012 11:45 pm

    Horse owners can tell you that botflies do exist in temperate places. We used to see their eggs all over our horses’ legs in the summer. They were little tiny yellow nits and they had to be scraped off with a blade.

  • Are there bot flies in Massachusetts?

  • Troy Meyers
    May 1, 2017 9:42 pm

    I wonder if you know why the halteres are so big, if they are really halteres, that is. Do they serve a different function in botflies than other flies?


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