After some testing, here is what works for me and reduces epidemics:

* Look at the queue of every building and receptionist all the time. If one building goes over 4, it's probably time to start thinking about building another building or hire more staff. When you use this approach, you don't need a lot of benches. One waiting room with 8 benches should be sufficient for a GP office. Other buildings only need 4 benches, or several rooms can share

* Hire the best staff. This will keep the queues lowest possible. There is a big difference between a consultant and a regular doctor, so I would even borrow money just to hire an available consultant.

* Put plants, toilets and drinking machines near the waiting rooms. This will separate the crowds from each waiting room.

* Put a GP office near every Diagnosis rooms. The max queue doesn't have to be large, just remember to reduce it if there is not enough space for plenty of benches.

Hi all,
Does epidemics hurts rep? I need 650 rep, and I'm stuck in the low 500 because of that machinery problem and epidemics. Is there any other way to increase rep ? I dragged prices to 96%, to no avail.
Thanks

This is a little late, but I've started playing again, and tested this. There was no change in reputation after I paid a fine or failed a cover up.

It seems like reputation increases naturally if you simply cure everyone that enters your hospital, so just play naturally and don't do things that will cause your reputation to drop, like failing a mission or sending alive people to the the autopsy.

Epidemics will happen a lot, but as mentioned, it will happen very rarely if some areas are not crowded. You can decrease the number of patients in a crowded area by building more buildings and increasing and decreasing the max queue of your buildings. The receptionists can't always be trusted.

I've attached the important aspects of my layout

This is a VERY aggressive plan of attack and you will go DEEP into debt (I was very very close to losing by having to large a negative balance). You need good staff and you don't want to kill anyone. SEND PEOPLE HOME. If you need a machine, don't be afraid to send people to research. You are going to depend on your end of year bonuses at first.

First, I build my training/staff research rooms after buying the two wings on the right. The first one is attached and is useful for diagnoses.

Research diag machines as fast as possible. You want a scanner and good GPs.

I build a triangle of GP offices (see image)

Next to the top GP's office, on either side, I build pharmacies.
I'm not sure if it's ALL but it certainly is most epidemics are cured in the pharmacy.

Between your main GP offices put a washroom so that anyone waiting in the main waiting area or in front of your pharmacies don't need to travel very far.

In the upper left, above where i have my Psychiatry room, i had a General Diagnoses and my inflator. I turned the general diagnosis into a clinic (either cast remover or slack tongue) as soon as i had the scanner researched and I was in the positive again.

STAFF:

Handymen:
Hire only the best handymen and set them to sweep. You want this hospital kept very clean. You will need to constantly monitor your machinery and page handymen to repair them. On the first of every month until you have slight overkill of handymen, check for more to hire. You want to be overstaffed.

Nurses:
Hire all the high skill nurses. You want them to be able to get across your hospital fast. Keep all nursing stations and clinics in the main wing of the building (ward, cast remover). Get all you can. Like handymen, you want overkill for nurses. If the advisor isn't complaining about it, you're doing it wrong. Luckily, epidemics will likely already be going in for a cure by the time you're notified. Highly skilled nurses should keep your patient volume low as they are close to your GP offices and entrance, as well as the fact that they deal with a wide variety of illnesses.

Doctors:

Hire all you can. Especially those with specialties. At the beginning of the game you should have at least a few consultants and as many medium to high skilled doctors as possible. You should also have a doctor with all three specialties. Pop him (and i think there's a researcher/psychiatrist) in with your consultant surgeon and train them in a nice training room with 4 seats, good size and lots of bookshelves. Once your surgeon/psychiatrist/researcher is a consultant, have him start training and set your surgeon loose on your hospital. You want to have too many doctors. Nice rooms, staff rest at no more than 40% and lots of videogames in your staff room. Keep your staff happy, when you're loan is maxxed out and you are still at 16,000$ in the hole, you won't be giving many bonuses or raises.

I can't stress enough. If you don't have a room for a cure, send a patient home. You don't want people milling about your hospital. Epidemics are a great source of income and following this plan it's a pretty easy source of income. The most contagious people I've had in my hospital which now turns a profit was 2 and they were both headed to the room.

The single square wide hallways on either side of the restroom are useful for bottlenecking contagious people in and putting a nurse in front of (as the nurse passes through them they should be vaccinated as long as you squirtied them).

When you have enough cures and money. Buy the rest of the wings and build the most expensive rooms to raise your hospital value.

Raising this thread up from the dead to ask you guys something: is there some way to force nurses to vaccinate infected people? They seem to do it randomly, even when I drop them right beside a waiting patient. This is driving me nuts!

Oh well, then I'll just have to hope they do their job properly! :D

There's also a cheaty way to avoid epidemics. When you hear the announcement and see the notice in the tray, immediately save and load the game. When you click on the tray icon, it will disappear without starting the epidemic.

Sorry for the bump, but just wanted to say a big thank you to everyone, especially MagicMagor, for the great advice. This is a really helpful thread.

Like probably many other players, I was doing well till I reached the first epidemics level. Then it was very chaotic and I just barely managed to finish it with some reloading and lots of luck. For the next level I took notice of the tips here (open waiting areas rather than narrow corridors + do the diagnosis and treatment rooms graudally as you need them/can afford them rather than chaotically all at once whenever you can). The next level went waaaaay more smothely. The few epidemics that happened were easily contained, or I just paid the fine; my hospital was going so well I could afford the money and reputation hit).
The only extra thing I did is hire 3 or 4 spare nurses. The assistant complains that I have too many of them, but when the epidemic comes they can vaccinate patients without disruption to their other duties; and their cost is pretty low.
Also, I used to always say yes to money demands; this time I noticed some doctors ask for outrageous sums, so it was cheaper to fire them. I had a constant supply of new cheap junior doctors in training room.

Also, turns out the room walls are very well insulated. I was placing radiators and turning heat to max till all the are on map was covered in red and wondering why do patients still suffer from cold. Turns out radiators in room do not heat the outside and vice versa. I now place a radiator in every room and in the "waiting room" areas outside.

There's an alternative way of stopping epidemics temporarily.

Delete all your reception desks. Sure, you won't be able to get new patients, but the health inspector wouldn't be able to inspect the hospital as well.

Sometimes it breaks the games and the epidemic notice won't end, but you won't get new epidemics either so I think this is a positive bug. =P

Also thank you for the hint regarding radiators. That I never knew. Makes so much sense. =)