TABLE 2.

Oligonucleotide primers used for cytomegalovirus DNA polymerase gene consensus and specific PCRs

Oligonucleotide	Orientationa	Locationb	Sequence (5′ → 3′)c	CMV sequence(s) amplified
DNA polymerase degenerate primers
CMV1F1	+	721–749	GAC AAG AAG TTG ACN ACN TTY GGN TGG TG	AmacCMV1, AsenCMV1, ApanCMV1
CMV1R1	−	1534–1559	ACG CCG GCY TCR TAR TGR AAR TTD AT	AmacCMV1, AsenCMV1, ApanCMV1
CMV1R2	−	1480–1504	CGT CCT GHA CRC ART AYT TNC CNA C	AmacCMV1, AsenCMV1, ApanCMV1
CMV2F1	+	1330–1352	GAY ATG TAY CCN GTS TGY ATG GC	AmacCMV1, AsenCMV1, ApanCMV1, PpitCMV1, SapeCMV1, SalbCMV1
CMV2F2	+	1372–1394	TAC AAR YTV AAY ACB ATG GCS GA	AmacCMV1, AsenCMV1, ApanCMV1, PpitCMV1, SapeCMV1, SalbCMV1
DFASAd	+	1768–1793	GTG TTC GAC TTY GCN AGY YTN TAY CC	All
CMV3F1	+	1795–1817	TCH ATY ATY ATG GCN CAY AAY CT	All
CMV3F2	+	2062–2090	ACG TGC AAT TCT TTY TAY GGB TTY ACN GG	All
CMV3R1	−	2269–2303	CGA TAG CAC ACA AAC ACR CTR TCN GTR TCN CCR TA	All
CMV3R2	−	2125–2147	CCG ATD CGN GTR ATR CTR GCC GC	All
CMV4F1	+	2266–2291	ATC TAY GGK GAC ACS GAY AGY GTS TT	AmacCMV1, AsenCMV1, ApalCMV1, AnanCMV1, ApanCMV1
CMV4R1	−	2782–2801	GCC GCY ARN CGY TTD ATG AC	ApalCMV1, AnanCMV1, ApanCMV1
CMV4R2	−	2477–2498	CGC ACC ARR TCR ACN CCY TTC A	AmacCMV1, AsenCMV1, ApalCMV1, AnanCMV1, ApanCMV1
CMV4R3	−	2419–2444	ATA TAC CGY TTY TTR CAG ATC ATC AT	AmacCMV1, AsenCMV1, ApalCMV1, AnanCMV1, ApanCMV1
DNA polymerase antisense specific primers (in combination with CMV2F1 or CMV2F2)e
PitR1	−	1958–1978	TGC GCT GAG CAA CCC ATT TAG	PpitCMV1
PitR2	−	1912–1932	ACG CAC CTC CGA CTT CAC AAA	PpitCMV1
AotR1	−	2019–2039	TTG TCG AGC AGC GTC CTC TTG	AnanCMV1, AvocCMV1
AotR2	−	1884–1904	ACC GTA CCG TTT TCG AAG TTA	AnanCMV1, AvocCMV1
SapR1	−	2106–2126	GCG ACT GGC AAA CAC GGT AAC	SapeCMV1
CapR2	−	1994–2016	GGG ATC TGT GCA ATC TTT CAT GG	CalbCMV1, CcapCMV1
CapR3	−	1939–1961	CGG GTC AAC AAT TCA GAA AGC AC	SapeCMV1, CalbCMV1, CcapCMV1
AteR1	−	1994–2016	CGG ATC TCT GCA ATT TTT CAT GG	ApanCMV1
AteR2	−	1935–1957	TCA GCA GTT CGG ACA ACA CTG AA	ApanCMV1
SaiR1	−	1948–1969	CCA CCC ACT TCG TTA GCA GCT C	SbolCMV1, SalbCMV1
SaiR2	−	2155–2175	ACG CGC GGT GTC TTG TAA CAT	SbolCMV1, SalbCMV1
AloR1	−	1959–1979	TTC CGT TGA GCC ACC CAT TTA	AmacCMV1, AsenCMV1, ApalCMV1
AloR2	−	1932–1954	GCA ATT CCG ATA GCA CTG AGG AA	AmacCMV1, AsenCMV1, ApalCMV1

^a+, sense; −, antisense.

^bPositions relative to ATG of the DNA polymerase gene of AoHV1 (accession number FJ483970).

^cLetters at positions of degeneracy follow the International Unit Base codes.

^dDegenerate oligonucleotide primer described by Rose et al. (46).

^eFor clarity, all antisense specific primers are indicated as XxxR1 for R1 primers and XxxR2 for R2 primers in Fig. 2.