I'd look for physical causes before mental ones. Yes, it isn't as much fun when the team players leave, but that shouldn't cause this noticeable of a problem. They ARE running a lot of miles. Going with the doctor running some tests sounds like a good idea to me.
It could be many things.
1.) Anemia. I'm no expert on fast running, but I am an expert on running while anemic, apparently. Last December I found out that I've probably been anemic for at least a portion of every month for the last few years (which probably started by having hypothyroidism which can cause very heavy and prolonged "cycles", but in December and January, I learned I have a large fibroid that really has exacerbated the whole losing iron thing to unimaginable levels. Enough where I was worried I might have to go the ER if I passed out). I don't want anyone to be anemic, but especially as a runner, I don't want myself to have to deal with being anemic and trying to run. It sucks.
I recently had surgery to remove a fibroid (this is a whole long fibroid story, but I was having very heavy iron loss every month since December, was on estrogen suppressing medication which successfully shrunk the fibroid Feb-June). I had an EKG before this surgery In July, and it showed I have an enlarged left atrium in my heart. This can happen inpeople with anemia and uterine fibroids, and I can only imagine what contribution the huge amount of running I do has had on this issue.
My point is, it could be anemia, and that is not something you want your son to be pushing himself very hard to keep up with the other boys if he has it, because it puts a whole lot of stress on the heart to keep sending oxygen to the muscles. It is like opposite doping, and when I stopped being anemic in March and early April, I found it so much easier to run up hills like I used to years ago.
2.) Overtraining syndrome or muscle soreness from weight lifting. It could also be that he is overdoing it lifting weights, and his body just needs more time to recover. In late May and early June I did too many "workouts" (Tempo runs, long runs, hilly runs and hill repeats) without giving myself enough recovery, and definitely noticed my whole body feeling sluggish and just not feeling up to my normal running speed or distance the following week.
Google "overtraining running", and you come up with "overtraining syndrome" - I believe this is from a Runner's World article:"One of the most common symptoms of overtraining syndrome is burnout. A runner who puts so much stress on his- or herself (think: poor sleep quality, caloric deficiency, and increased anxiety about an upcoming race) will feel spent. Mental fatigue is often overlooked, but it is an important part of training."
The reason the coach is having him rest a week might possibly be from burnout.
As for "bulking up", sprinters usually have more muscles which help them run very fast. Long distance runners (including cross country) usually have much leaner muscle mass because any extra muscle weight that doesn't help them run is extra weight in general which can slow them down. If his 3 x a week weight lifting sessions are bulking him up, this might be adding unnecessary weight as well as causing muscle damage. In order to build muscle, you must cause muscle tears, which can cause inflammation and soreness, and from my own experience, whenever I've done enough weight lifting (we are talking body weight squats and lunges and 24 pound total deadlift - I am no body builder and apparently pretty weak), I end up with DOMS which definitely slows my running down when I'm running sore.
3.) Not heat adapting well. It could be that his body is not becoming heat adapted as quickly as the other boys on the team. Runners can adapt to running in very hot temperatures and this usually takes about two weeks. It still won't be as efficient or have as fast of times as running in cooler temperatures. My body is definitely not heat adapting properly this summer (but I'm still currently on or just coming off the last injection of Lupron Depot, which suppresses estrogen. So basically, I have hot flashes upwards of 15-20 times a day - and running turns in to just one giant hot flash where it feels about 15 degrees warmer than it is. This was fine it February, and if my surgery had been in May when it was supposed to be, that would have been great. Running in 80 degrees now is awful.)
What difference does temperature make? Back in March, my average easy run pace was around 11:30 per mile. I'm slow, but I also have some health issues and I run because I like running, not to race anyone else. Now, with 80 degree temperatures, even before surgery my average easy run is around 12:15/mile. Post surgery is even slower, but it has been a lot hotter.
And on the topic of heat adaptation, I hope he is getting enough electrolytes. It has been in the 80s here, and I have been "intuitive electrolyte supplementing" - normally I run with water and do electrolytes after the run at home. The last several days, I have been running with water and electrolytes, and then if I feel like I still need more, taking more when I get home. As much as some might think that eating a diet with salt in it is enough to replenish electrolytes, if I am too low, I wake up with fingers swollen like sausages and deal with twitching or cramping muscles.
Has he been tested for covid? More than once, as there are so many false negatives? We're in a pandemic and he's fatigued. Might not be a coincidence. I doubt anxiety would slow anyone down. I've had it for a long time and it had no effect at all on my athletic performance. The meds we take for it do, though. Sometimes you get used to them and sometimes you don't, but they are all sedating. Unless you're feeding him terribly, anemia is probably not it, but a doc will test for everything if it's a good doc. Have you asked him? Given what you've said about him, is it possible it's his mood? Depression is much more likely than anxiety to have such an effect. Has his sleeping changed? And it could just be he's aging out of running and aging into something else athletically. People who are good at things when they are very young aren't usually good at it as they age, which is why elite athletes get very few in number.
My husband, a runner, also added that if the faster runners are allowed by the coach to ditch slower runners and go off by themself, that's bad coaching. He thought the coach should do some trade-ups of "pace leader" so everyone gets a small group to be the pace leader of, and they trade off that role. The faster runners will get just as good of exercise even when they aren't running their top speed, and they can do some fartleks too.
[Description of fartleks: " After a warmup, you play with speed by running at faster efforts for short periods of time (to that tree, to the sign) followed by easy-effort running to recover. It’s fun in a group setting as you can alternate the leader and mix up the pace and time. And in doing so, you reap the mental benefits of being pushed by your buddies through an unpredictable workout. If you’re running solo, you can use it as a playful way to pass the time by targeting random markers as the finish line for the hard efforts. The goal is to keep it free-flowing so you’re untethered to the watch or a plan, and to run at harder efforts but not a specific pace."]
Anyway, not to repeat the (much more) excellent advice you've gotten above, but I'd suspect a physical problem first and would check for things not so obvious like Covid and Lyme disease and anemia. If that is all negative, I'd wonder if it was a mental thing, like he's burning out on running in general. After that, I'd question whether it's an emotional thing, like he doesn't feel welcome in the group any more. Teenagers do sometimes just change their mind about liking something enough to keep doing it, especially when there is a fine line between it being fun and it being boring and hard. Something might have made it cross that line.
Good luck figuring it out.
Fartlek, despite what one might assume, means "speed play" in Swedish. When my husband and his running friends began doing fartleks in the 1980s, I couldn't help but wonder if they did them mostly because they liked to say the name.