If a parasitic creature was discovered, how would officials determine whether that parasite was a new species or an existing parasitic species? How long would that process take?

Assume the species is discovered in livestock (risking the food supply) first and then in the farmers who own that livestock (meaning it can infect multiple mammalian species, not just cattle or people). The creature in question isn't an obvious parasite like heartworms or tapeworms, but something new (or new to America at least), spreading, and so far as the initial discoverers can discern, 100% fatal. (So there's incentive to fast-track the process.) It is macroscopic by the time symptoms appear, but it's larval stage is microscopic.

I've been able to find notes on how long it takes to do forensic DNA analysis, but that's different; the goal there is to identify characteristics to find out who a person is. They already know the species -- human. And that process depends on how backlogged the lab that runs the tests is. And I know how long it takes veterinary labs to perform DNA tests for known species -- identifying avian influenza, for example. Those tests take between 1 and 5 days for the lab to carry out sample prep and testing for a known species.

I can't seem to find data for ruling out known species and then determining a new one.

Assume America and basically modern day/modern levels of real-world science.

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    $\begingroup$ ...They don't do DNA tests to determine the type of parasite someone is hosting... They check the immune response of the host and look at the physiology of the parasite. $\endgroup$
    – AngelPray
    Sep 2 '17 at 19:01
  • $\begingroup$ @AngelPray - that is true if the appearance of the parasite gives them any clues. If not, next is DNA; see below. $\endgroup$
    – Willk
    Sep 2 '17 at 19:52
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    $\begingroup$ Why not asking this on biology stackexchange? $\endgroup$
    – L.Dutch
    Sep 3 '17 at 4:39
  • $\begingroup$ Your question is tagged [tag;hard-science], this is entirely unnecessary. It should be science-based, please edit it accordingly. $\endgroup$
    – a4android
    Sep 3 '17 at 13:27
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    $\begingroup$ Something which is fatal to the host is technically a pathogen, not a parasite. Parasites have a vested interest in keeping the host alive as long as possible $\endgroup$
    – Thucydides
    Sep 3 '17 at 22:09

I'm majoring in Ecology & Evolutionary Biology, Microbiology, and Bioinformatics. I have a textbook about gene sequencing right next to me, coincidentally, so I hope I can help out a bit.

DNA sequencing is not a go-to for identification of eukaryotic organisms (or for most pathogens at all). But if your parasite has garnered government attention, CDC would get on identification very quickly with state of the art high-throughput sequencing.

High-througput DNA sequencing is fast. A whole human genome can be assembled with automatic programs (which could take a day) and additional human analysis (which could take 3-4 days). So that's around 4-5 days with leading sequencer technology.

DNA sequencing that is used to identify organisms doesn't assemble a genome. DNA fragments are compared with various genome databases to identify the organism, or what it is most closely related to, which is a much faster process (~6 hours?). Having a whole genome doesn't tell you much once you've assembled it, especially if there are no similar organisms in the genome databanks, so for identification purposes, you don't need to assemble a genome. If it's from another country and that deadly, it's very likely to make world news and the CDC would already be tracking it asap--especially if the US is close to this country.

Additional opinions, feel free to disregard if you've got your critter all figured out:

A parasite is an organism that relies on a host to survive and can often go undetected and cause very little harm to its host. Often it is in the best interest of the parasite not to kill its host, because it needs the host. A parasitoid is an organism that has a parasitic relationship with its host but specifically results in death of the host. Usually that indicates the parasitic organism no longer needs a host to reproduce at that stage of its life cycle. A pathogen is a disease-causing organism that causes notable damage to cells, but the term isn't usually applied to macroscopic things.

I would suggest basing it off of an existing organism--this will save you grief of researching the plausibility of various aspects of your critter, and also amplify the creep-out factor. There are some super terrifying weird things out there, like the parastic screw worm fly, which was eradicated from the US--but came back!

Also, it would be incredibly bizarre to suddenly have a eukaryotic parasite outbreak if it's spreading at the rate that it is. Deadly emerging diseases are usually viruses or bacteria because these can mutate much faster and produce new strains, unlike eukaryotic organisms. The reason many of these have high mortality is because they are relatively new strains that have not before infected humans. This is a trend seen with infectious diseases, and usually levels out in mortality after a few years because, again, it is often in the pathogen's best interest to keep its host alive.

I enjoy worldbuilding my own pathogens.

  • $\begingroup$ Hello ULTRAVIRULENCE, and welcome to Worldbuilding. It's great that you enjoy worldbuilding, but in encouraging people to contact you directly, you also deprive others of the chance to provide (and learn from) such questions and their associated answers. For that reason, I have deleted that passage from your answer. However, I absolutely do encourage you to look through tags that interest you and post answers where you feel you can contribute something not already mentioned in existing answers. Enjoy your stay! $\endgroup$
    – user
    Sep 3 '17 at 9:09
  • $\begingroup$ While it's true that "Often it is in the best interest of the parasite not to kill its host", this is only useful in the long run. An initial outbreak is not constrained in this fashion. My understanding is that syphilis is a classic example. $\endgroup$ Sep 3 '17 at 14:01

from http://www.nejm.org/doi/full/10.1056/NEJMoa1505892#t=article: Malignant Transformation of Hymenolepis nana in a Human Host

This man had a cancer, but the malignant cells were not human cells. In an effort to diagnose what it was these scientists used a shotgun approach with PCR vs many different species specific DNA sequences. They were surprised to get back the result that these were tapeworm cells. Then they used immunohistochemical tags specific to tapeworm cells, as well as sequenced tapeworm DNA. This was a cancer derived from tapeworm cells. About as freaky a thing as I have ever read about. I did not know humans could be infected with nonhuman cancers!

Excerpts from the article below.

This case posed a diagnostic conundrum. The proliferative cells had overt features of a malignant process — they invaded adjacent tissue, had a crowded and disordered growth pattern, and were monomorphic, with morphologic features that are characteristic of stem cells (a high nucleus-to-cytoplasm ratio) — but the small cell size (<10 μm in diameter) suggested infection with an unfamiliar, possibly unicellular, eukaryotic organism. Infection with a plasmodial slime mold (phylum, Amoebozoa; class, Myxogastria) was considered because of the prominent syncytia formation. Although many cestode tissues are syncytial — notably, their tegument — a tapeworm infection was initially considered less likely because of the primitive appearance of the atypical cells, the complete absence of architecture that was identifiable as tapeworm tissue, and the rarity of previously reported cases of invasive cestodiasis.2,3


Molecular Identification and Confirmation We performed Myxogastria and panfungal PCR assays in an attempt to target an unknown eukaryote, but these assays unexpectedly identified H. nana with 99% sequence identity. The presence of H. nana DNA in the specimen was confirmed by cestode- and hymenolepidid-species–specific PCR testing and sequencing. The molecular findings were surprising, since there was no recognizable tapeworm tissue architecture; thus, to confirm that the cells originated from a tapeworm, we performed immunohistochemical studies and in situ hybridization, which localized cestode antigen and nucleic acid markers

So: if this is in the modern day you would extract DNA from the unknown parasite and shotgun with primers corresponding to various candidate organisms which might be related. That worked here - their kit must have included tapeworm even though that was not on their short list of candidates. But maybe the kit has nothing close to your parasite. If so, you would sequence segments of the new organisms genome which are conserved across the various kingdoms (e.g. fungal, slime mold, arthropod, cestode) and compare the gene from the new parasite with gene sequence from known creatures. Closest gene homology would mean closest relative. Then you could confirm with immunohistochemistry appropriate for the organism type, as the authors did here. The authors also confirmed via DNA sequencing that the malignant cells had mutations which correspond to cancer-driving mutations known in human cells.

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    $\begingroup$ There are incorrect details in this answer (e.g. cestodes form a class not a kingdom) regarding phylogenetic determinations, and those details should be cleared up, this answer does have the right general thrust and is a more currently accepted method than using Koch's postulates, Koch was long dead by the time the DNA revolution got underway. $\endgroup$
    – DPT
    Sep 2 '17 at 20:59

The parasite can be microscopic or macroscopic. If macroscopic, it will be picked up trivially during the post-mortem -- if the disease is widespread enough then you can be absolutely sure that very rigurous autopsies will be performed.

If the parasite is microscopic then read on...

Long live the memory of Robert Koch

Robert Koch was a German physicist and a pioneer of microbiology; for hist discoveries he got the Nobel prize for medicine in 1905. His four postulates were the first formulation of the criteria for establishing a causative relationship between a microbe and a disease; quoted from Wikipedia:

  1. The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms. (The second part is no longer required today, because we have learned that the immune system can very well kill or fight to a standstill most pathogens.)

  2. The microorganism must be isolated from a diseased organism and grown in pure culture.

  3. The cultured microorganism should cause disease when introduced into a healthy organism.

  4. The microorganism must be reisolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent.

Today we (that is, epidemiologists and microbiologists) used a much more refined set of rules, named the Bradford Hill criteria. But the essence is what Koch said in 1890.

So what the microbiologists do when confronted with a new disease which has an unknown pathogen? (Warning, this works for a story but not necessarily in real life, and I'm definitely not a microbiologist.)

  1. First, make sure it's an unknown pathogen. They will run tests for all known pathogens which cause similar symptoms. If they come up empty, then they will proceed to step 2.

  2. They will want to see where the pathogen hides itself. For this, they will try to infect experimental animals with various parts of the diseased animal -- blood, lungs, brain etc. Let's say that it hides in the pancreas.

  3. They will then proceed to an detailed microscopic examination of the organ, looking for stuff which shouldn't be there. If they find such stuff, they are all set for isolation, else they must work harder.

  4. They slice and dice the victims' pancreases, and try to grow cultures on various substrates with various nutrients. In parallel they will also try to see whether the pathogen can pass through an ultrafilter; if it does, it a virus, if it doesn't it's a bacterium (or possibly an eukaryote such as the horrifying Plasmodium).

  5. Once they have identified the pathogen they will compare it to known microbes or viruses; they will use both microscopic observation and DNA comparison, and will announce the discovery.

How long does it take? From a few weeks to several years, depending on the diseases, the pathogen, the luck of the researchers etc.


They will use taxonomy. It's a centuries-old science, used to identify species. First, they examine specimens of the organism, try to see whether it matches known species, and then use molecular biological assay techniques to further identify, if needed, its place in evolutionary history. This is normal science. Nothing fancy at all.

In the comments it is noted that this question doesn't need the to answer it. This is not a answer accordingly.


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