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Choanal atresia

Choanal atresia, often referred to as CA, is one of many congenital and presumed to be hereditary defects in llamas. It is of little or no short-term concern to average llama owners, but of great importance to llama breeders, and to those llama owners who would someday like to have one or two offspring from their female working animal(s). However, even those who would like to own only a couple of geldings can be affected -- both partial CA and crudely corrected CA llamas have been sold without disclosure to unknowledgeable buyers.

Wiping out CA is not as simple as culling producers. Choanal atresia involves at least one recessive gene, and thus can remain hidden in the gene pool indefinitely without the help of an affordable DNA test to detect carriers.

Interestingly, the other species afflicted with CA is humans. Identifying CA carriers and the reponsible genes in llamas may allow insight into the nature of the defect in humans.

What is choanal atresia?

Choanal atresia is a congenital condition (meaning that the llama is born with it) in which the normal airway (between the nasal and pharyngeal areas) is blocked by bone, membraneous tissue, or a combination of the two. Occasionally, only one passage is blocked (unilateral) or the blockage is not complete. Both of these conditions are referred to as "partial choanal atresia."

CA occurs in both North and South America, in all climates, and under many different management systems and practices (or lack thereof). CA occurs more frequently in llamas related to those already known to produce offspring with CA. The combination of the preceding conditions and the obvious familial relationships indicates that the condition is hereditary. It has also been established that males and females are affected with equal frequency, that there must be at least one recessive gene involved in the inheritance mechanism, and that a CA carrier can inherit the defective gene from either a male or a female parent.

CA also occurs in alpacas, indicating that the responsible mutation in lamas is probably a very old one. CA occurs only rarely in other domestic species, and the cause in those species is unknown. CA does occur in humans, however, is hereditary, and is often accompanied by other defects.

What happens to a cria born with choanal atresia?

Although mild partial CA crias may merely seem less active than their peers or even go undetected until adulthood when work demands result in inexplicable shortness of breath, a full (bilateral) CA cria must breathe through its mouth, and thus cannot nurse without also getting milk into its lungs, which in turn results in life-threatening pneumonia. A CA cria's nostrils usually flare with each breath. It may gasp for air, or it may barely have its mouth open, leading the observer to incorrectly deduce that it is breathing through it's nose. One method of quick diagnosis is to hold the mouth and one nostril tightly closed and see if the remaining nostril fogs a mirror (at room temperature); the procedure is then repeated with the other nostril. A blocked nasal passage will not be able to fog up a mirror, and a CA cria will also be stressed (and quite distressed) by this test.

CA crias frequently have other defects, such as heart and other internal organ defects, missing kidney or portions of the reproductive system, partial or complete lack of olfactory structures (that is, the cria cannot smell), and occasionally polydactyly (extra digits).

Although there are two surgical techniques to provide the cria with a nasal airway, neither are entirely satisfactory. One is a crude and difficult-to-control technique that involves punching holes in the blockages via the nostrils under sedation. If the cria is lucky enough not to be speared through the brain by the "tool," tubes are inserted into the nostrils so that the new openings will not heal shut. The long-term problem with this technique is that at birth, the tool used can only be as big around as a pencil. This does not provide an adequate airway for an adult llama to pursue a normal life.

A second technique for correction is a surgical reconstruction of the nasal passages. This provides an adequate airway, but involves months of tedious and difficult aftercare to ensure proper healing without infection. In addition, the necessary approach disturbs four growth plates, and so the adult corrected llama has a shortened upper jaw. This means that molars do not meet correctly, incisors jut out beyond the bite plate and upper lips, and comfortable use of a halter is compromised. This second surgery is very expensive, apparently is a painful result for the adult llama, and is only used for those llamas necessary for CA research breeding herds.

Not yet tried (to our knowledge) is opening the nasal passages using an endoscope and laser surgery, allowing the llama's skull growth plates to mature, and only then proceeding with surgical reconstruction.

When one considers the drawbacks to the current methods of surgical correction and the important fact that a CA cria stands a good chance of also having other, very serious undiagnosed defects and may die anyway (after a crummy life of intestive medical treatments), the most humane choice usually is, unfortunately, immediate euthanasia.

How frequently does choanal atresia occur?

The only universally accepted answer is that estimates vary!

  • One source states that 25% of all alpaca deaths in South America are due to choanal atresia, and that in South America, all alpacas are considered probable carriers. (note: This is patently ridiculous, as any simple, lethal recessive gene with a 100% carrier rate would result in 25% CA crias, who then die ... and so then all the other alpacas would have to be immortal for that math to be accurate! Nonetheless, we were contacted by a prominent camelid researcher, requesting that we locate the study and original data for him ... which proved to us, once again, that people with DVMs and PhDs don't necessarily have any common sense.)
  • One North American study compiled data showing that choanal atresia accounted for 10% of all congenital defects seen at the institutions contributing to the survey.
  • Of singly-tabulated defects, only umbilical hernias (a non-lethal defect) occured more often than CA.

Another North American study estimated that a CA carrier bred to randomly selected llamas would produce a CA cria in one out of 30+ matings. This implies that, depending on the mode of inheritance, CA might be carried by anywhere between one in eight and one in three llamas in the population. Current evidence favors two forms, each caused by a different single recessive gene (and perhaps also activated by a single copy of a separate, dominant gene), and thus a one-in-four figure might apply, but at a rate approaching something more like one-in-eight (each carrier would have to be of the same type to produce a CA cria). By extrapolation, then, CA would occur in one out of every 240 births.

Some informal surveys indicate that this is a fairly reasonable estimate. Some breeders (particularly those fortunate enough not to have had CA crias) think that estimate is too high. Several others with large herds (as well as recent informal surveys) agree on a 1-in-100 births figure. Of course, one thing that is certain is that figures gleaned from breeder surveys and from institutional databases are definitely skewed (low) by those who choose not to report or reveal the birth of CA crias.

What llamas are known producers of CA?

Unfortunately, the subject of CA producers is a big can of political worms. In the past, when fancy woolly llamas had pricetags of five and six figures and stud fees were commonly $1000 to $6000, any CA cria meant a large outright economic loss. Neutering the parents was simply not considered by the investment-driven llama multipliers. The vast majority of CA producers were simply bred to different llamas in hopes that another choanal atresia cria would not be the result. Big-ticket stud owners made threats, paid what amounted to hush-money, objected to making registry records public (which -- back then when all females were kept pregnant all the time -- would show mysterious gaps in a female carrier's production followed by matings to a different male), and made public statements that CA was carried only by females or could not possibly have a genetic basis. If the cria was born on their own farm, the policy was "shoot, shovel, and shut up." CA-producing females were frequently the first to be sold off (without disclosure) to unsuspecting buyers. Unfortunately, during this time, some very prolific and popular studs were also carriers, and thus the frequency of choanal atresia carriers within the llama population markedly increased.

The current situation is different -- llama prices are a lot lower, for one thing -- but economics still gets in the way of the truth. There is an oversupply of llamas, and so multipliers (and real breeders) are finding it difficult to meet the llama bills by selling the llamas that they raise. Many are frightened that if they reveal one of their animals had a CA cria, nobody will buy any of the related llamas on their overcrowed farm, or related animals on their friends' farms. Those who provide stud service have spent a lot of money to advertise and promote their stud, have taken in (and already spent) a lot of money from stud fees, and thus are frequently unwilling to lose their ride on the gravy train (or merely risk lawsuit from past customers) by revealing carrier status.

Some people do disclose the names of CA producers that they own, or owned and have since neutered and sold. For now, this is the best a prospective buyer can hope for. Once a test for CA carriers has been developed, a buyer would be foolish to consider purchasing any llama (other than a gelding or spay) that has not been tested.

How can I make sure that I don't by a CA producer?

Until a test becomes available to determine carriers, you cannot be sure. For now, llama breeders are limited to stacking the odds against it through knowledge of the llama's geneology.

Everybody makes their own decisions regarding how much risk they are willing to take -- that is, how many generations back they feel comfortable allowing a known CA producer to appear in their breeding stocks' pedigrees. Some people will not accept a known CA producer anywhere in the pedigree of a breeding animal; others are comfortable with 3-5 generations; still others are content to own and breed half and full siblings to known producers. Those who breed close relatives of CA producers such as full siblings and normal-appearing offspring of known producers are increasing the odds that they or their progeny's buyers will end up with a CA cria. Virtually all ethical breeders agree that this is an irresponsible practice unless the resulting offspring are neutered.

The one exception to "staying away from close relatives" is throroughly researched male ancestors of a CA producer. Those studs who have already had numerous normal offspring -- particularly by any females who later produced a CA cria or carrier -- are at a very low risk for being carriers themselves. Matings to 30+ different females would be a bare minimum; 60 or more healthy cria would be a reasonable indication that the stud is not likely to be a carrier. It is possible for a stud to be a carrier and to not produce a CA until after 100 or more offspring, but the odds against it are rather high. Offspring of male ancestors who pass this close scrutiny (unless they are out of the same female that produced the carrier) are also comparatively low risks.

It would be inappropriate to test any descendent of a CA producer in this manner because it not only risks making more carriers, but adds to the current oversupply of llamas. However, male ancestors may have produced enough offspring to make on-paper research possible without any actual impact on the llama population.

How do I make safe mating choices to be certain that I don't have a CA cria?

Until a test for carriers is available, you simply can't be certain. If the possibility of a CA cria is too devastating for you to consider, then the only thing you can do is to not breed llamas, or at least not breed llamas until the carrier test has been developed.

You can attempt to breed only from llamas who are not related to CA producers, but this practice is only as good as your knowledge. Furthermore, your knowledge is only as good as your sources' honesty -- owners of the most prolific CA producers tend to keep tightly sealed lips and may lie when asked direct questions. Finally, a CA carrier female may go an entire lifetime without producing a CA cria. Carrier status is more easily passed undetected through female lines by virtue of the fact that the females produce fewer offspring.

What should I do if a CA cria is born in my herd?

This will vary somewhat depending on your proximity to adequate veterinary diagnostic facilities, but the primary concern should be to first confirm that you do in fact have a CA cria. A cria may also have trouble breathing for other reasons, and the mirror test can be conducted improperly, giving both false hopes and fears. Positive diagonsis is by contrast radiography (the cria must be sedated) or endoscopy.

You can aid in choanal atresia research by obtaining a minimum of 5ml whole citrated blood samples for DNA research (Texas A&M will in turn extract leucocyte pellets -- which have very high quality DNA -- from the samples and freeze them).

If you do not own both parents or are uncertain of the cria's parentage, obtain 5ml EDTA whole blood (in a lavendar top tube) so that you can have DNA fingerprinting done through the International Lama Registry for parentage confirmation (or exclusion). Parentage of defective crias produced from outside breedings is often contested or denied by the stud owner. You need solid (DNA) proof of parentage to protect you from liability and slander suits (and possibly fulfillment of a breeding contract or a refund). And if by some chance the sire is actually an animal you own, such as a young male on your farm that you thought was too young to breed or a llama you were sure couldn't ever get over or through his fence, then you will have important, invaluable information about your own animals and their genetic material.

After obtaining adequate samples, euthanize the cria (unless you have chosen to pursue corrective surgery) and allow the mother some time with the body to help her accept her loss. If you are not donating the cria's body for research (we do recommend at least obtaining a necropsy with a written report), allow the body to remain until the mother walks away on her own. Remember to milk out the colostrum from the mother and freeze it. You or someone else in the area may need it someday.

It is courteous to inform all buyers of descendants from the CA producing parents, and the owners of all grandparents of the CA cria. If you do not own the stud, inform the stud's owner immediately and allow him or her to inform anyone who owns relatives of the stud. Contacts should be made prior to any public disclosure of the CA producer(s) that you own. However, none of these people has a right to request or demand that you make no public disclosure, or to restrict the information you disclose. As long as you have a written necropsy report and parentage confirmed by DNA analysis, you may disclose all facts about the situation without fear of lawsuit (some stud owners do threaten to sue, but no lawyer would take the case as long as you have the necropsy report and the DNA analysis).

Public disclosure of CA producers you own (registered name and ILR number) will help other people make their breeding and purchasing decisions. Public disclosure may turn up other related producers and make the line of inheritance clear, absolving many noncarrier relatives of undeserved blame. We do not recommend listing grandparents of CA producers in a public forum because those animals may be wrongly misunderstood to be the carriers themselves. Good forum for disclosure are some of the lama listservers; you may also disclose on this page (below) by emailing us the information and asking that we post it, or you may do so on your own webpage (we'd be happy to link to it).

If you do not own the sire, you should not disclose his name or owner unless you have (1) DNA fingerprinted the cria, sire and dam and thus proven beyond doubt that the named stud is in fact the sire or (2) received written permission from the sire's owner. The ramifications, if you chose to ignore these precautions, could be a very expensive lawsuit along with political blacklisting that is very difficult for a breeder to survive. Believe us -- it HAS happened to many people.

If a CA cria is born in my herd, what should be done with the parents? How about other relatives?

Virtually no one will argue that both parents of your CA cria should be immediately and permanently removed from the gene pool, preferrably by sterilization. More than a few people will balk at such a suggestion, however, if it is their breeding stock that is on the line.

This is what we have done, and recommend:

The male parent is castrated. If you will retain both ownership and possession of the female parent, spaying may not be necessary (for some females, being open is stressful and/or distracting, and those llamas should be spayed if possible). If the female might be sold, leased or loaned, she is spayed first. Even if you sell her to a good friend whom you can trust, situations change and she may later be resold, this time to someone who does not understand (or care) about the important responsibility breeders have to cull carriers of genetic defects, or circumstances (such as death or mental incapacity) may prevent your good friend from making full disclosure.

A conscientious breeder with adequate funds (and space) could theoretically opt to leave a superior animal intact and not breed him or her until the carrier test is developed. Potential mates could then be screened and only noncarriers used to produce a worthy, noncarrier replacement for the carrier parent; all carriers produced in the process would be spayed and castrated. However, in practice, this would only be worth considering if the producer is undeniable superior and irreplacable in all other aspects. Between the expense of having to test all offspring, the numerous spays that would be necessary, and -- if the carrier is male -- the lost production from all of the (presumably excellent) noncarrier females tied up in the effort to produce that one replacement, using any CA carrier for breeding in this manner would not be economical. It also would not be approved of by those who are unable to understand that any carriers produced would be sterilized, and thus a breeder might suffer further economic loss through a needlessly damaged reputation. And, most importantly, the necessary test is still in development -- and funding is proving more and more difficult to obtain for political reasons.

Other relatives are a tricky matter. As outlined above, the research possibilities for ancestors are much different than for descendants. Decisions are best made on a case-by-case basis. A good policy for immediate descendents is to not breed them until a carrier test is available so that their status can be determined.

How can I protect myself and minimize my own economic losses in case one of my llamas has a choanal atresia cria?

  • Select and breed from only those animals with a valid end use. Llamas who can no longer breed but can pack, show, drive, or fulfill some other function will retain value.
  • Preserve females' physical integrity by not impregnating prior to maturity (see female breeding age). Females who are not bred until after physical maturity can still pack, show, or drive, and thus retain much of their value.
  • Do not breed your female to an outside stud or purchase a bred female without a contract specifically outlining recourse in the event of a choanal atresia cria ("genetic defect" is not sufficiently clear wording). Be sure the accepted method of proof is also in writing.
  • Do not offer stud services or sell bred females unless you cannot afford to provide a full refund in the case of CA births. Designate what proof will be necessary (eg, documentation of necropsy by a veterinarian and DNA parentage verification) in the event of an alleged CA cria. It may sound overly cautious to insist on parentage verification and veterinary documentation, but what if the father is actually a weanling male on the dam owner's farm? It has happened. What if the dam owner or his/her veterinarian had never seen a CA cria and mistakenly put down a cria with pneumonia? You certainly wouldn't want to castrate your stud and refund monies in either case. For both provided stud service and sales of bred females, also put in writing what steps both parties will take regarding the female parent -- any refund by the stud owner should be contingent on permanent, surgical removal of the dam from the gene pool.
  • In both sales and purchase contracts, include a "full disclosure" clause that entitles both parties to full disclosure regarding named defects in the particular animal's history (including relatives) before sale, and also indefinite rights by both parties to futher disclosure in the event that additional information becomes available after the sale.
  • Be aware that you can't realistically expect a purchase contract to guarantee a given animal is not a carrier of choanal atresia. Discovery of genetic defects that cannot be tested for (and that's all genetic defects in llamas at this time) is one of the many risks inherent in the process of breeding animals. For the same reason, do not offer contracts that guarantee a given animal is not a carrier of choanal atresia unless you can afford to fulfill those contracts to all buyers' complete satisfaction.
  • Once a test for carriers becomes available, demand that all llamas (except geldings and spays) be tested prior to purchase (have blood drawn in your presence by a veterinarian you've hired and mail the sample yourself), and also insist that any deposit monies be fully refundable if the animal in question is found to be a carrier. You may wish to waive testing if both parents have been tested and found not to be carriers, however, be aware that the possibility of record or identity falsification will exist, and that false positive and false negative results occur in other tests. The true accuracy of a CA carrier test won't be known until after years of use.

How can I help find the genetic marker and develop a test for choanal atresia?

  • Send blood samples from the cria and both parents to DNA researchers at Texas A&M. Chilled whole citrated blood (5ml minimum) is preferred unless your vet is able to extract frozen leucocyte pellets (5ml). Ship chilled samples on melting ice at 4° C (do not ship over a weekend or a holiday) and call if you or your vet have other questions: (409) 862-4402
L. Garry Adams
Department of Veterinary Pathobiology
Medical Research Building, Foom 103
Hwy 60 W
College of Veterinary Medicine
Texas A & M University
College Station, TX 77843-4467
  • Provide full known geneology of both CA-producing parents to researchers when providing samples or a cria. Disclose names of CA-producing llamas in appropriate public forums and state that you have provided geneology to researchers -- this example encourages others to follow suit.
  • DNA fingerprint any CA cria with questionable parentage, or who was the product of one or more llamas that you do not currently own.
  • Donate money to organizations currently funding choanal atresia research, such as Morris Animal Foundation, or make donations directly to Oregon State University (make checks payable to The OSU Foundation ). Be sure you make a notation that the money is to be used for choanal atresia research in llamas.
Morris Animal Foundation
45 Inverness Drive East
Englewood, CO 80112-5480
Oregon State University
Dean's Office
College of Veterinary Medicine
200 Magruder Hall
Corvallis, OR 97331

Based on what is already known about the lamoid genome and similar research in other species, it can be stated with reasonable accuracy that it will take three to five years to locate the genetic marker for choanal atresia. Once the marker has been found, however, it will take relatively little time to develop a test that will identify CA carriers.

After a test becomes available, the burden of eliminating CA from the gene pool rests squarely on the shoulders of breeders and buyers. Within two generations, noncarrier offspring from any superior carrier parents can be selected as substitute breeding stock and there should be no reason to breed from a CA carrier. However, without incentive from buyers and preferably changes in registration policy, some people will refuse to test their breeding stock and may even knowingly continue breeding carriers.

Although DNA research is not cheap, unlike most other very important llama research, once the marker for CA has been found and the test developed, there will be no more research expense. Another point is that even with our modern technology, we can only learn how best to reduce occurances and provide treatments for most other llama afflictions -- total prevention is not an option. Genetic defects, such as choanal atresia, can be all but eradicated. For these two reasons, the money spent on choanal atresia research is not wasted, but rather is well-spent towards a tangible, permanent end.

The good news is that with education, effort, commitment, and a valid carrier test, llama breeders could be successful in completely removing choanal atresia from the North American registered llama gene pool. Without a test -- and lack of funding and cooperation are the major reasons why there IS no test yet -- carriers will continue to spread the genetic material for CA throughout the gene pool, eventually making eradication impractical or impossible. Those who have experienced the joy of having healthy llama companions and yet have also seen the heart-wrenching struggles of a CA cria followed by the disappointment of euthanizing the newborn and then neutering one or more of their carefully selected breeding animals know more than anyone just how important a CA carrier test is to the future health and viability of the entire llama species.

Further reading:

Medical information

  • Choanal Atresia, Smith and Timm, Llamas Magazine, Nov/Dec 1994
  • Congenital/Hereditary Conditions (in Medicine and Surgery of South American Camelids), Fowler, 1989
  • Congenital Defects in the Llama (in Veterinary Clinics of North America: Update on Llama Medicine), Leipold, Hiraga, and Johnson, 1994

Opinion pieces

  • The Problem with Choanal Atresia, McGrath, Llama Life II, Winter 1997-98


On December 22nd, 1997, we had a CA cria born on our farm. We owned both parents at the time.

  • Sire: Hidden Valley Silverhawk, ILR #59424 [has been castrated; all decendents have been neutered]
  • Dam: Rocky Mountain Kiowah, ILR #118507 [has been spayed; no other offspring]

If you would like disclose of any choanal atresia producer(s) that you own for inclusion in the above list, email for details about submitting information and proof of ownership. Your name will not be included in the posting unless you request it.

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