Below is a list providing examples of the many different specimen types can be used for the detection different viruses by electron microscopy (EM). Despite the explosion of rapid, molecular diagnostic methods, EM still plays an important role in the detection of new and emerging viruses and structural classifictaion of existing viruses.

Virus Clinical Specimen
  Adenovirus Throat swab/washing; Stool extract; Human brain; Liver
  Astrovirus Stool extract
  Calicicvirus Stool extract
  Coronavirus Stool extract; Nasopharyngeal secretion
  Cytomegalovirus Urine; Liver; Lymp Node
  Hepatitis A Stool extract
  Hepatitis B Serum
  Herpesvirus Lesion fluid; Scab; Brain
  Influenza Throat washing
  Minireovirus Nasopharyngeal secretion; Stool
  Mumps virus CSF; Nasopharyngeal secretion
  Norwalk and Norwalk-like Stool extracts; Vomitus
  Papovaviruses Urine; Brin homogenate; Brain; Wart extract; Laryngeal papilloma
  Parainfluenza virus Nasopharyngeal secretion
  Parvovirus Serum
  Poxviruses Lesion fluid; Crusts; Smears
  .........Vaccinia
  .........Orf
  .........Molluscum contagiosum
  Rotavirus Stool extracts
  Respiratory syncytial virus Nasopharyngeal secretion
  Small round viruses Stool extracts
  Varicella-zoster Skin lesions; Brain; CSF

Data extracted from:
L.Soshiro, S.E.Miller, Application of Electron Microscopy to the Diagnosis of Viral Infections, in Laboratory Diagnosis of Viral Infections, 2nd ed. (E. H. Lennette), Marcel Dekker, Inc., New York, New York, 1992, Chapter 2.