First, my thoughts are with those who are dealing with these issues. You were wondering in earlier posts about "what next" and "what did you do after culling"....I had the unfortunate experience of contracting ILT in my flock last year. Through various testing at our provincial vet/agricultural testing facility it was determined that the ILT virus strain was from the SHEDDING virus vaccination, and made it's way into my flock when I unknowingly added one of these vaccinated birds to my coop. Since the rest of my surviving flock would be carriers of the shedding virus for life, the only logical and ethical choice was to cull the entire flock if I had any desire to interact with other poultry keepers (ie friends with farms), sell or show birds. So, we culled every bird. Pets, favorites, rarities, all of them. It was emotionally very difficult, but in the end, the only choice we had if we wanted to continue on with the fancy. We cleaned, scrubbed, pressure washed with an antivirucidal cleaner (we used Virkon, I'm not sure if you can get that in the States...we are in Canada), burned all bedding/shavings, burned then buried the culled birds, shoveled out 4 inches of topsoil from the outdoor run and buried it, discarded anything possible including leftover feed. Discarded brooms and disinfected all tools/gear/feeders/waterers...anything that could have been exposed to the virus. Repeated cleaning the coop and gear again in a month. Left the coop clean and unpopulated until the following season. Repeated the antivirucidal cleaning. These steps were what the provincial and federal avian vets suggested to minimize the risk of infecting any new birds with the virus. It was a lot of work, heartache, not to mention the monetary loss. Now that we are through it, I am glad that we took the time to do things properly and we are in a position to start all over again.
In order to minimize risk in the future, we are now only obtaining new stock through hatching eggs. We are keeping a somewhat closed system, where no chicks/adult birds enter the property. We are vaccinating for mareks and ILT. It was also suggested that we consider vaccinating for Newcastles and Infectious Bronchitis.
Unfortunately, another friend and poultry keeper was going through a similar situation and we came up with this strategy....she would cull most of her birds, keeping the best breeders and favorites to obtain eggs from. Once my facility was clean, she shipped eggs to me. I immediately discarded all packaging off site and disinfected the eggs using a special egg dip treatment (link to Tylan dip treatment
http://www.poultryswapontario.net/forum/viewtopic.php?f=56&t=468 . Eggs were set and incubated in a brand new hovabator incubator as normal. Chicks hatched and immediately put into vaccination program, and raised in a brooder in our garage for many weeks until the chicks could have time to build immunity. After the recommended period, chicks were reintroduced to our coop. My friend who donated the eggs is actually in the process of moving to a new farm. Next year when she is established at her new site and the birds are laying I will send her eggs to restock. In this way, all of the genetic lines were saved and we can both move ahead with a clean flock. We are also doing a regular blood testing program with the local agricultural vet college in order to monitor flock health more closely.
I share this just so that you guys can know there are others out there who have gone through similar situations. It is so hard. But it will get better. There are ways that you can save your genetic lines - you won't be able to save your favorites/pets, but will have their offspring. Try to look for the positives (through testing you will know what you are dealing with; you will become more informed about these diseases) and move forward with whatever strategy is best FOR YOU, and YOUR goals as a poultry keeper. There aren't really any right or wrong answers as everybody has their own personal husbandry and management ideas/goals.
I thank you and commend you for being open and honest about your situations so that others can learn along with you. I'm sure that if you choose to cull and start again there will be many generous people here on the forum that will even be willing to donate hatching eggs if and when you are ready to move forward.