Coccidia is a protozoal parasite.
It can cause loose, foul smelling yellow, sometimes blood tinged stools. But it doesn't usually cause nausea, vomiting or lethargy.
It is an opportunistic parasite meaning that in a healthy adult dog it generally is quickly gotten rid of an causes no symptoms.
With overcrowding and poor sanitation it can become an issue.
It tends to cause symptoms in the very young, old or dogs that are sick from other disease processes because their immune systems are weak.
In most cases symptoms of lethargy, nausea, and loss of appetite is triggered by eating something they should not, too much table food, too many treats or something they find outdoors.
More serious causes of vomiting at this age include toxin ingestions, viral or bacterial infections, or a full or partial gastrointestinal obstruction.
In a young dog, especially if he never finished his vaccine series, a viral infection such as Parvo virus, toxin ingestion, or a foreign body leading to a partial or full gastrointestinal obstruction would be the most likely cause of what you are seeing.
If he isn't bouncing back he may need to be hospitalized for fluids, antinausea medication and supportive care to get him on the right track.
If that isn't possible for whatever reason tonight there are some things we can try at home, but if he's not improving quickly he should be rechecked and have some diagnostic testing done, intravenous fluids and injectable medication to settle his stomach.
To try and settle his stomach at home you can give either:
1) Pepcid ac (famotidine) at dose of one half of a 10mg tablet per 10 to 20 pounds of body weight every 12 hours
2) Prilosec (omeprazole) at one quarter of a 20mg tablet per 10 to 20 pounds of body weight every 24 hours
These are acid reducers and may help settle his stomach and get him feeling better and hopefully get his appetite back.
In a couple hours to get some electrolytes in you can offer him a 50:50 mix of pedialyte and water.
Then offer a bland diet of 1/3 boiled, minced, white skinless chicken or boiled, lean hamburger and 2/3 boiled, white rice mixed with some low salt chicken or beef broth to make it easy to lap up and swallow. If he refuses that you can offer a little meat baby food. If he refuses both then don't push it, he needs veterinary care.
But if things go well and he does eat and doesn't vomit feed him the bland diet for 2 to 3 days then slowly start to mix back in his regular food, a little more at each meal. It should take about 5 to 7 days to slowly convert him back to his regular diet.
If he continues to eat poorly and be lethargic even with the acid reducers, runs a fever (more than 103F rectally), or has a lower then normal temperature (less then 99F), has a tense painful belly or if he refuses to eat he should see a veterinarian for an examination, diagnostics, injectable anti-nausea drugs intravenous fluids and supportive care.
Heart murmurs in young puppies can signify a serious congenital heart defect too. If his heart isn't pumping blood efficiently he won't get proper oxygen to his brain and organs, which certainly can lead to lethargy. I would consider a consult with a veterinary cardiologist to look into that.
Please let me know if you have any further questions.