The eye swab medium was thawed, and 125 μl of the liquid was
added to 125 μl minimal essential tissue culture medium plus 2%
fetal calf serum. To this mixture was added an equal volume of 0.02 M
Tris, 0.01 M EDTA, and 1% sodium dodecyl sulfate (SDS), to which 100μ
g/ml proteinase K was added. The solution was incubated at 37°C
for 90 minutes, and the DNA was separated by two extractions in
phenol-chloroform-isoamyl alcohol (25:24:1) followed by one extraction
in chloroform-isoamyl alcohol. The DNA was precipitated at room
temperature for 15 minutes by addition of a 0.1 volume of 3 M sodium
acetate (pH 5.2) and a 0.6 volume of isopropyl alcohol. The DNA was
concentrated by centrifugation at 12,000
g for 20 minutes and
the DNA pellet washed with 70% cold ethanol, dried in a vacuum, and
dissolved in 50 μl of water. To 25 μm of the DNA sample was added
10 mM Tris-HCl (pH 8.3); 0.75 mM Mg Cl
2; 50 mM
KCl; 2.5 U
Taq DNA polymerase; 250 μM each of dATP, dCTP,
dTTP, and dGTP; and 25 picomoles of each primer nucleotide in a final
volume of 50 μl. The primers used were based on the polymerase gene
of the 17syn + HSV-1 strain.
8 The 23-base 5′-primer
(sense) oligonucleotide(CGGACTCCATCTTTGTGCTGTGC) was from
nucleotides65,466 to 65,489 in the unique long segment of the
DNA sequence, and the 23-base 3′-primer (anti-sense) oligonucleotide
(AAAGTCCTGGATGTCCCTCTCCG) was from nucleotides 65,877 to
65,900
9 ; both primers were synthesized by Integrated DNA
Technology (Coralville, IA).
The reaction volume was overlaid with 2 to 3 drops of mineral oil, and
the DNA was amplified using a thermal cycler (model 480; Perkin–Elmer,
Foster City, CA) programmed for 35 1-minute cycles of denaturation at
96°C, a 2-minute 67°C annealing step, and a 2-minute 72°C primer
extension step followed by a 7-minute 72°C delay step. Controls for
the DNA amplification included 100 ng HSV-1 strain 17syn + DNA
(type-specific positive control) and distilled water (negative
control). Fifteen microliters of the amplified reaction material was
applied to a 2.5% agarose gel, and the amplified DNA was visualized by
staining in 0.5 μg/ml of ethidium bromide in water. DNA of known size
(base pairs) were run in parallel to confirm the size of the amplified
product.
The sensitivity of the PCR reaction was determined in two ways. First,
serial dilutions of infectious HSV-1 were prepared in transport medium,
and the DNA from each was extracted and the PCR reaction performed
identically with the procedure used for the actual eye swab cultures.
This showed that the extraction process coupled with the PCR could
detect 200 pfu of HSV-1 (data not shown). Second, the sensitivity of
the PCR reaction was determined by adding known quantities of purified
DNA to the PCR reaction cocktail. This showed that the PCR itself could
detect 100 fg of viral DNA after ethidium bromide staining and visual
inspection of an agarose gel (data not shown). Because PCR is
notoriously sensitive to contaminants, in preliminary experiments, we
added serial 10-fold dilutions of rose bengal or lissamine green B from
1% to 0.00001% to mock swab preparations before extracting the DNA.
In separate experiments, we added serial 10-fold dilutions of the dyes
to known amounts of HSV-1 strain 17syn + DNA in the reaction mixture
before thermocycling the preparations. Under both circumstances,
neither dye diminished detection of viral DNA (data not shown).
The specificity of the PCR reaction for detection of HSV-1 was
confirmed by using the described primers in separate reactions
containing DNAs from HSV-2 strains HG52pl8, MS, and 186; herpesviruses
EBV, VZV, and herpes saimiri; and adenovirus types 2, 5, 7, 8, 9, 10,
11, 13, 19, and 37. No product of the expected 434-bp size was detected
in agarose gels or by Southern blot hybridization using a 32P-dATP–labeled HSV-1-specific DNA probe (data
not shown). However, when the primers were used in reactions containing
HSV-1 DNA from strains 17syn +, KOS-63, KOS-79, + GC, and H129, the
predicted 434-bp fragment was seen in agarose gels and by Southern blot
hybridization.