With gastroenteritis, total WBC isn't raised, the only abnormality is low lymphocytes (339). Is this likely a virus, or an autoimmune condition?

Gastroenteritis. Most gastroenteritis is viral and lasts only a few days at most. Often it lasts only 24-48 hours. The total WBC count is not usually elevated. A low lymphocyte count is normal during such an infection. Here's a research paper describing this phenomenon, called "transient lymphopenia" : http://www.Ncbi.Nlm.Nih.Gov/pubmed/1085751.