People get sick more often in the winter because virus molecules travel better in dry air. In moist air, the virus molecules tend to latch on to water molecules and get diffused out of the air. So, step one is to put a humidifier in your room when you sleep. If your house is very dry in the winter, see if your parents will get a whole house humidifier. The one for your room is cheap. The one for the house is more expensive.
Otherwise, you are young. Your immune system is still developing. It is very common for high school age kids to come down with a pretty bad respiratory illness in the winter. As noted by others, improving your diet is always a good thing, regardless of any propensity for respiratory illnesses. But, the main thing you should try to do is to make sure you eat and sleep. Do not skip any meals. Do not skimp on a meal (candy bar for lunch, coffee and donut for breakfast). And be sure to hydrate a fuel up right after running. Viruses attack when you are weak. Skipping a meal is a great way to make yourself vulnerable to a virus in the winter. Sleep is also a great way to fight illness. Make sure you get at least a solid 8 hours a night. 9-10 is better for a growing teenager. Cut of all electronics an hour before you want to do to bed. If you are going to stay out late, do it on weekends when you can sleep in. Sleep deprived=sick. Lastly, dress warmly, especially on a run. Shed clothing if you have to. Getting a chill is another thing that will weaken your system and invite attack from viruses.
If you really want to be vigilant, wear a surgical mask in the winter. Your classmates will flip out and give you all kinds of sh=t, but it does help diffuse out germs.