Possibly a respiratory infection, but the whining sounds more like she's inhaled something. I've had a few cases of that, one recovered within 48 hours (still have her) --- she was braying like a donkey with every breath, unable to walk more than a few steps for oxygen starvation --- and the other died, well, with assistance, because over the course of about a week she got worse and worse and worse until she was blue in the face, really struggling for breath, and clearly dying by increments. So it was a mercy cull.
Common cause is feeding loose dry feed, especially something they love and scoff madly, or right when they're really hungry. Dry husks, cracked grains, powdered feeds, and small seeds like millet are primary causes in my experience.
A couple of times a year I'll have a chook sneeze loudly after inhaling millet, generally young ones as they learn to not scoff it so quickly, but wetting down or soaking the feed cuts the risk enormously, and over my years of chicken keeping there's only been those two cases that had an issue with having inhaled something. I've kept many hundreds of chooks by now, so it's not a large percentage that had issues. I also don't know that it was the feed in their cases at all. I soak it almost as a rule anyway, helps bind powdered additives or smaller particles to the larger ones, enables them to gain much more nutrition from the grains, etc...
Hydrogen peroxide can do wonders for clearing the respiratory system, especially for shifting very deep seated infections. You can give it to the hen neat or add it to the general water. That will also help if it's a contagious problem. You'd need the plain and diluted (or dilute it yourself) hydrogen peroxide, not the stuff they've added toxic agents to in order to prevent its use as anything other than cleaning fluid; one drop will help but a couple more is better, but it doesn't take much at all to help.
If this is an inhaled foreign object rather than virus or fungal infection or whatever, though, hydrogen peroxide might not be too useful. After all the fluid buildup in the case of a foreign object would ideally help her shift it on a sneeze and reducing that could be counterproductive. Just a possibility, not a guarantee.
Raw garlic, recently minced or crushed, is also great at disinfecting the mucosal membranes of the body, it has over 30 natural and powerful antibiotics in it and is fast-acting. It can help prevent respiratory issues from developing and help clear existing issues. So can slippery elm bark powder but that's more expensive and probably better used on a case by case basis.
If you suspect this may be contagious then dosing all the flock with raw garlic would be ideal to bolster their immune systems and tackle the infection.
One to two cloves per hen is a good start and you can keep it up for a week, or only a few days, or whatever suits. I feed it regularly. Adding it to yoghurt can help get them to eat it if they don't like it to start with, but in the case of respiratory infection processed dairy is worth avoiding because it does make respiratory infections worse in a lot of animals. So you could try adding it to their normal feed, as in soak the garlic with the grains so they get the taste of it (they generally take a day or two to make up their mind about new dietary additions in my experience), which will also ensure each hen gets some into her system even if she only eats the grain. My hens pick it out, I used to think maybe some would miss out because of that, but each hen takes as much as she feels she needs and individual needs fluctuate over time, so everyone gets some. They do self-medicate, given a chance.
If this is something inhaled, as it sounds like it is, it's pretty deep by the description you gave, not higher up the respiratory tract like my survivor hen's case, and she's obviously in a bit of trouble and there's not really anything you can do except hope she expels it, sorry.
If she's not eating I wouldn't worry about it for one or two days but any longer is a concern. If she's not drinking at all, that's a bigger issue and might be a vet case if you can afford it. Some people have even injected fluids into the lower bowels of chickens to hydrate very desperate cases.
If you think it's a viral/fungal/bacterial cause, then any one of the things I mentioned could help, or artificial antibiotics may; you can even safely and with benefit use garlic, hydrogen peroxide, slippery elm and artificial antibiotics in conjunction with one another. Garlic boosts the efficacy of artificial antibiotics.
Anyway, not a good scenario, but I hope she makes it.
Edited by chooks4life - 2/27/15 at 6:56am