Table 2. Core diagnostic testing algorithm for the Emerging Infections Program Encephalitis Project, 1997–2010*.

Pathogen	Specimen type	Test type	Seasonality
Viruses
Adenovirus	NP swab	PCR	Year-round
Arbovirus panel†	Serum	Serology	May–October
Enteroviruses	CSF	PCR	Year-round
	NP swab	PCR	Year-round
	Rectal swab	PCR	Year-round
Epstein-Barr virus	CSF	PCR	Year-round
	Serum	Serology	Year-round
Herpes simplex virus 1 and 2	CSF	PCR	Year-round
Human herpesvirus 6	CSF	PCR	Year-round
Influenza virus A and B	NP swab	PCR	November–April
Parainfluenza virus 1–3	NP swab	PCR	November–April
Rotavirus	Rectal swab	Antigen	November–April
Varicella zoster virus	CSF	PCR	Year-round
West Nile virus	CSF	Serology	May–October
	Serum	Serology	May–October
Bacteria
Bartonella spp.	Serum	Serology	Year-round
Chlamydia pneumoniae	NP swab	PCR	Year-round
Ehrlichia spp.	Whole blood	PCR	May–October
	Serum	Serology	May–October
Mycoplasma pneumoniae	NP swab	PCR	Year-round
	Serum	Serology	Year-round
Rickettsia spp.	Serum	Serology	May–October
Treponema pallidum	CSF	VDRL	Year-round
	Serum	RPR	Year-round

*Diagnostic testing algorithm at the Tennessee site; regional differences and testing availability associated with minor variations in core testing at the California site. Additional supplementary testing was performed when indicated based on individualized epidemiologic, demographic, clinical, or radiographic features. CSF, cerebrospinal fluid; NP, nasopharyngeal; VDRL, venereal disease research laboratory test; RPR, rapid plasma reagin.
†Arbovirus panel included Lacrosse virus, St. Louis encephalitis virus, Western equine encephalitis virus, and Eastern equine encephalitis virus.