analysis of acquired human cytomegalovirus infections by
TRANSCRIPT
JOURNAL OF CLINICAL MICROBIOLOGY, Sept. 1993, p. 2433-24380095-1137/93/092433-06$02.00/0Copyright © 1993, American Society for Microbiology
Analysis of Acquired Human Cytomegalovirus Infections byPolymerase Chain Reaction
JAMES F. BALE, JR.,12* MARSHA E. O'NEIL,1 SARAH S. FOWLER,1 AND JODY R. MURPH'Departments of Pediatrics1 and Neurology, 2 The University ofIowa
College ofMedicine, Iowa City, Iowa 52242
Received 12 March 1993/Returned for modification 3 May 1993/Accepted 7 June 1993
We used the polymerase chain reaction and primers corresponding to three regions of the humancytomegalovirus (HCMV) genome to study HCMVs isolated from 16 children attending a single day-care centerand the father of two children in the same center. When we analyzed isolates with primers for the pp65 andmajor immediate-early genes, we observed nearly uniform amplification yielding products of predicted sizes.By contrast, primers for the a sequence demonstrated variability among HCMV strains, supporting the use ofthese primers as an epidemiologic tool. Analysis of a-sequence products from two isolates demonstrated 50 to70% nucleotide homology with the a sequence of HCMV Towne strain DNA. We observed 95% nucleotidehomology for the two a-sequence products derived from the father-child pair. Analysis of day-care centerisolates indicated that two children excreted two distinct HCMV strains during the study interval.
Children in group day-care centers in the United States,the parents or caretakers of such children, and adults withmultiple sexual partners acquire human cytomegalovirus(HCMV) at rates that greatly exceed those of the generalpopulation (3). Rates of HCMV infection among day-carecenter workers, for example, range from 8 to 20% annually(4) versus 1 to 5% among persons lacking such exposures.Although the majority of these acquired infections do notproduce disease, HCMV can cause an infectious mononu-cleosis syndrome in previously healthy individuals and mayinduce serious, life-threatening disorders in persons withimpaired cell-mediated immunity (8).Recent reports (6, 7, 12) indicate that the polymerase
chain reaction (PCR) can be used to characterize the geneticvariability of the virus, suggesting that PCR has potential asa method to investigate HCMV transmission. We used PCRwith primers corresponding to three regions of the HCMVgenome to study HCMV isolates derived from one largegroup day-care center. Our results indicate that PCR with ana-sequence primer can be used to characterize the epidemi-ology of HCMV transmission and provide additional evi-dence that children in group day-care centers can be rein-fected with distinct HCMV strains.
MATERIALS AND METHODSHCMV isolates. The virus strains analyzed in this study
consisted of HCMVs isolated between May 1986 and March1991 from (i) 16 children in a single large day-care center (19total isolates distinct from those in prior reports [14]) and (ii)the father of two children in the above-mentioned center(one isolate). HCMV was isolated from this parent after theonset of hepatitis attributed to HCMV. The HCMV Townestrain was propagated separately as a positive control forPCR and restriction enzyme analysis.Primary HCMV isolations were achieved by incubating
urine or saliva on confluent monolayers of human foreskinfibroblasts (HFFs) grown in 24-well plates in 5% CO2 at37°C. Monolayers were fed with Eagle's minimum essentialmedium containing 10% fetal calf serum, 50 U of penicillin
* Corresponding author.
per ml, 50 ,ug of streptomycin per ml, and 50 ,ug of genta-micin per ml and observed weekly. All isolates exhibited thecharacteristic HCMV-induced cytopathic effect, and 15 iso-lates were further confirmed by immunofluorescent stainingwith an HCMV-specific monoclonal antibody (MicroTrak;Syva Company, Palo Alto, Calif.).PCR analysis. DNAs extracted from HCMV-infected HFF
monolayers were amplified by PCR with five separate sets ofHCMV primers (Table 1). Reaction mixtures for typical PCRamplifications consisted of 1.25 U of Taq polymerase, 200,uM each deoxynucleoside triphosphate, 50mM KCl, 10 mMTris-HCl (pH 8.4), 1.5 mM MgCl2, 100 ,ug of gelatin per ml,20 pM each primer, and approximately 1 ,g of target DNA ina final volume of 50 ,ul. Typical PCR parameters consisted ofan initial denaturation for 2 min at 94°C, which was followedby 25 to 40 cycles of denaturation for 30 s at 94°C, annealingfor 30 s at 55°C, extension for 1.5 min at 72°C, and then afinal extension for 10 min at 72°C.
Controls for each run included amplification of (i) purifiedviral DNA extracted from HFF monolayers infected with theTowne strain of HCMV (courtesy of Mark Stinski, Depart-ment of Microbiology, University of Iowa), (ii) DNA fromuninfected HFFs, and (iii) buffer with sterile, distilled H20replacing target DNA. In several experiments, DNAs werecoamplified with primers for beta-globin DNA (10) as aninternal PCR control (primer 1, 5'-GGTTGGCCAATCTACTCCCAGG-3'; primer 2, 5'-GCTCACTCAGTGTGGCAAAG-3'; product size, 536 bp). Appropriate precautions weretaken to prevent contamination.For initial size analysis, 8 ,u1 of each PCR product was
studied by electrophoresis in 1.8% agarose gels (SeaKem;FMC Corp., Rock Island, Ill.) run at 30 V for 4 h. Molecularsize markers (123-bp ladder; Bethesda Research Laborato-ries, Gaithersburg, Md.) were incorporated in the initial andfinal lanes of each run. Gels were recorded by Polaroidphotography, and bands were scored by two readers (J.F.B.and M.E.O.).The specificities of PCR products were determined by
Southern blot analysis with HCMV probes specific for thetarget region. Amplification products were separated on0.9% agarose gels run at 60 V for 2 h and were transferred toZetabind membranes (CUNO, Inc., Meriden, Conn.) by
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TABLE 1. Primers for detection of HCMV genes
Size (bp)Primer Sequencea of pre-dicted
product
a sequencebA
Primer 1 TTC CCC GGG GAA TCA CAC AG 130-220Primer 2 TTT TTA GCG GGG GGG TGA AAProbe GCG CCOG CAC GTC GCT TTT AT
IE-scPrimer 1 CCA CCC GTG GTG CCA GCT CC 159Primer 2 CCC GOCT CCT CCT GAG CAC CCProbe CTG GTG TCA CCC CCA GAG TCC
CCT GTA CCC GCG ACT ATC CIE-m
Primer 1 TTG GOCC GAA GAA TCC CTC AA 404Primer 2 TCT GOCA AAC ATC CTC CCA TCProbe GAT TAA GGT TCG AGT GGA C
pp65Primer 1 TAG GTG ACC AGT ACOG TCA AG 223Primer 2 TCC AGC ATG ATG TGOC GAG ATC TProbe AAG CTC TTT ATG CAC GTC A
pp65bPrimer 1 AAA GAG CCC GAC GTC TAC TAC ACOG T 159Primer 2 CCA GGT ACA CCT TGA COGT ACT GGT CProbe GTT CTC CAT GGA GOCA AAC CAG CTC
GTG COGCa Oligonucleotides 5' to 3'.b From Zaia et al. (22). The probe for a-sequence products was derived
from the nucleotide sequence of isolate 311u.c From Shibata (15).
using a vacuum transfer apparatus (Red-Evac; Hoefer Sci-entific Instruments, San Francisco, Calif.). Membranes wereprehybridized according to the manufacturer's instructions.Bound DNAs were hybridized with the appropriate probesend-labeled with [_y-32P]ATP and were visualized by autora-diography.
Restriction enzyme analysis. Several virus strains werestudied by modifications of methods described previously(14). After three or four passages in HFFs, viral genomic andcellular DNA was harvested by proteinase K digestion,chloroform-phenol extraction, and ammonium acetate-etha-nol precipitation. DNAs were resuspended in sterile H2O,and the concentration was adjusted to 1 ,ug/,lI by the additionof H20. DNAs were stored in H20 at 4°C until used.For restriction enzyme analysis, 1 to 3 ,ug of DNA was
incubated with EcoRI or HindIlI overnight at 37°C in theappropriate buffer. Digested DNAs were separated by elec-trophoresis on 0.8% agarose gels for 2 h at 100 mA andtransferred to Zetabind membranes (CUNO, Inc.), and themembranes were prehybridized for 3 h by procedures de-scribed by the manufacturer. Bound DNA was then hybrid-ized overnight with an HCMV probe, theXbaI D fragment ofHCMV Towne (courtesy of Mark Stinski) labeled with[32P]dCTP by random priming, and visualized by autoradiog-raphy. This probe spans part of the long repeat, all of theshort repeat, and part of the short unique regions of theHCMV genome (20). Our methods correspond to the junc-tional hybridization approach described by Spector et al.(18).DNA sequencing. Selected PCR products were sequenced
by the University of Iowa DNA Facility by using fluores-cence automated DNA sequencing and an Applied Biosys-tems (Foster City, Calif.) model 373A automated DNA
bp
492-
246-123-
-536
-223
ml 3 5 7 9 11 13m
FIG. 1. Amplification of selected HCMV isolates with pp65primers. Shown are an ethidium bromide-stained gel (top) and acorresponding autoradiogram with a 32P-labeled probe (bottom).Lanes: 1, no DNA (control); 2, HFF DNA; 3, HCMV Towne DNA;4, 368s; 5, 310u; 6, 365s; 7, 380u; 8, 356u; 9, 356s; 10 and 11, 369s;12, 311s; 13, 311u. m, molecular size marker lanes. The 536-bpproduct in this and Fig. 2 to 4 corresponds to the amplificationproduct of the beta-globin gene primers.
sequencer according to instructions provided by the manu-facturer. The volumes of PCR reagents were doubled toprovide 50 to 100 ng of PCR product in a final volume of 100,ul. Primers were provided at a concentration of 0.8 pm/ul.Hardcopy sequence data were reviewed and compared withrespect to HCMV strains.
RESULTSPCR analysis. Amplifications with one or both pairs of
primers for the pp65 gene yielded predicted products for allbut one HCMV isolate (344u). Amplifications with the IE-sprimer, corresponding to exon 4 of the major immediate-early gene, resulted in uniform products for all but fourisolates (329u, 344u, 356u, and 361u). However, a productwas observed when 329u and 361u were amplified with theIE-m primer (corresponding to exons 3 and 4 of the majorimmediate-early gene), suggesting that these isolates con-tained nucleotide variations in the region of the IE-s primer.The nucleotide sequences of the primers used in theseexperiments are indicated in Table 1, and representativeamplification products are shown in Fig. 1 and 2.
In contrast to the above-described results, considerablepolymorphism was observed among HCMV isolates (Fig. 3)when analyzed with the a-sequence primer described byZaia et al. (22). The isolates yielded a-sequence products ofthree sizes: approximately 220 bp (group A), approximately180 bp (group B), and approximately 130 bp (group C). Theproduct derived by amplification of purified HCMV TowneDNA was intermediate in size between group B and Cproducts.By using this schema, seven day-care isolates could be
classified as group A, three could be classified as group B,and three could be classified as group C. Two additionalisolates, shown in Fig. 3A, lane 11, and Fig. 3B, lane 5, hadfaint bands that appeared to categorize them as group Astrains. Four isolates, shown in Fig. 3A, lanes 9 and 12, andFig. 3B, lanes 9 and 13, had no a-sequence products. One ofthese isolates (364s) had a faint product on a duplicate run(Fig. 3B, lane 5), suggesting that it was a group A strain,whereas a group C product was observed in one run for 369s.
Beta-globin coamplification products were identified in the
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PCR ANALYSIS OF ACQUIRED HCMV INFECTIONS 2435
Abp
Z5
m 1 2 3 4 17 l9 1 1112S114 mm l 3 5 7 9 11 13 m
FIG. 2. Amplification of selected HCMV isolates with IE-mprimers. Shown are an ethidium bromide-stained gel of PCR prod-ucts (top) and an autoradiogram with 32P-labeled probe for the IE-mamplification product (bottom). Lanes: 1, no DNA (control); 2, HFFDNA; 3, HCMV Towne DNA; 4, 319u; 5, 318u; 6, 375u; 7, 312u; 8,364s; 9, 364s; 10, 378u; 11, 361u; 12 and 13, 329u; 14, 368s. m,molecular size marker lanes.
runs for three of the negative isolates (361u, 364s [Fig. 3B,lane 9], and 369s), and elimination of the beta-globin primersgave similar results (data not shown). The three isolates haddetectable products when amplified with an IE or pp65primer. Thus, we believe that the results for these strainsindicated nucleotide variations in the a sequence sufficient toinhibit PCR amplification.When the groups of isolates were compared according to
the dates of sample acquisition, it was found that group Aisolates were recovered between November 1988 and March1991, group B isolates were recovered between April 1988and November 1988, and group C isolates were recoveredbetween May 1986 and March 1988 (Table 2). The twoisolates that had faint bands suggesting that they were groupA strains were isolated in October and December 1987.Isolates without a-sequence products were recovered be-tween December 1987 and June 1989. Thus, categorizationby a-sequence product size generally correlated with tem-poral clusterings of isolates, a feature compatible with hor-izontal transmission ofHCMV strains in the day-care center.Three sets of paired isolates obtained 12 or more months
apart from each of three children were among the isolatesanalyzed in this study (Fig. 3 and 4). Two children (311 and356) appeared to excrete two distinct strains during the studyinterval. Child 356 appeared to excrete a group A strain insaliva in 1987 (Fig. 3A, lane 11) and a group B strain in urinein 1988 (Fig. 3B, lane 11). Child 311 excreted a group C strain(Fig. 3A, lane 7, and Fig. 4, lane 2) in saliva in 1986 and agroup A strain (Fig. 3A, lane 14, and Fig. 4, lane 1) in urinein 1989. A group A strain isolated in 1989 was also excretedin urine by the father of child 311.Comparison of PCR and restriction enzyme analysis. We
next compared the restriction endonuclease fragment pat-terns of several group A isolates. These results, shown inFig. 5, suggested that at least two strains (isolates 368s and378u) were closely related. The pattern shown by theseisolates was similar to the pattern of the group A strainsexcreted by child 311 and his father. One isolate (356s) hada distinct restriction enzyme pattern differing from that ofother group A strains by at least four bands in the combineddigests.
Bbp
492369246
123
ml 2 3 4 5 6 7 8 9 1011 1213M
FIG. 3. Amplification of HCMV isolates with a-sequence prim-'ers. (A) Lanes: 1, no DNA (control); 2, HFF DNA; 3, HCMVTowne DNA; 4, 329u; 5, 368s; 6, 310u; 7, 311s; 8, 365s; 9, 344u; 10,380u; 11, 356s; 12, 369s; 13, isolate from a congenitally infectednewborn; 14, 311u. m, molecular size marker lanes. (B) Lanes: 1, noDNA (control); 2, HFF DNA; 3, HCMV Towne DNA; 4, 319u; 5,364s; 6, 318u; 7, 375u; 8, 312u; 9, 364s; 10, 378; 11, 356u; 12, 368s;13, 361u. m, molecular size marker lanes. A, B, and C in the rightmargins correspond to the sizes of a-sequence products, as de-scribed in Results.
The a-sequence products from several group A isolateswere further characterized by digestion with restrictionenzymes BssHII and Mnll (data not shown). We observedidentical digestion patterns for isolates 368s and 378u (cut byBssHII but not by MnlI), supporting the conclusion thatthese strains were closely related. The a-sequence amplifi-cation product of isolate 365s had a similar digestion pattern,whereas 369s did not.
Sequence analysis. We performed sequence analysis of twoa-sequence products. This analysis demonstrated approxi-mately 95% nucleotide sequence homology between isolatesfrom child 311 and his father (Fig. 6A), group A strainsknown to have similar restriction enzyme profiles. Com-pared with the published nucleotide sequence for the HCMVTowne DNA a sequence (11), the clinical isolates exhibited50 to 70% homology. The isolates demonstrated approxi-mately 90% homology in the a-sequence pac-2 motif, con-
serving the six-nucleotide sequence (5'-TlTlTAT-3') (Fig.6B).
DISCUSSIONOur results indicate that a-sequence primers have utility in
investigations of HCMV transmission. We observed that
bp
492-369-246-
123-
-536-404
492369246
123'Wz.0, .IW-
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TABLE 2. Summary of HCMV isolates and PCR results
Isolate' Date (mo/day/yr) of PRgoPsample collection PCR group"310u 11/16/88 A311u 6/14/89 A356s 10/02/87 A (faint)364s 12/08/87 A (faint)365s 11/16/88 A368s 11/16/88 A375u 2/20/91 A378u 2/22/91 A380u 1/04/91 A318u 4/21/88 B329u 5/19/88, 6/15/89 BC356u 11/07/88 B311s 5/13/86 C312u 5/20/86 C319u 3/30/88 C344u 6/14/89 NPd361u 1/08/88 NP364s 12/08/87 NP369s 11/16/88 NPIsolate from father 4/07/89 A
of child 311
a Numbers correspond to designations for children in the day-care center.s, saliva; u, urine.
b Determined according to the product size (in base pairs) when the isolatewas amplified with a-sequence primers. A, approximately 220 bp; B, approx-imately 180 bp; C, approximately 130 bp.
c On initial size analysis bya sequence. On a subsequent run (Fig. 4), a faintgroup A band was seen in the autoradiograph.
d NP, no product. In one run, a faint group A product was seen for 364s anda faint group C product was observed for 369s.
HCMV isolates can be grouped according to the sizes of thea-sequence products and that strains with similar-size a-se-quence products tended to cluster temporally in the day-carecenter, suggesting that these strains were horizontally trans-mitted. Transmission of certain group A strains was further
bp,:
56...5369246
123-ml1 2 34 56 7 8910m
B 0 : -
1 23 678910
FIG. 4. Amplification of HCMV isolates with a-sequence prim-ers. (A) Ethidium bromide-stained gel of PCR products. (B) Auto-radiogram with a 32P-labeled probe for a-sequence products. Lanes:1, 311u; 2, 311s; 3, 356s; 4, 310u; 5, 329u; 6, HCMV Towne DNA;7 and 8, blank; 9, 11FF DNA; 10, no DNA (control). m, molecularsize marker lanes.
A
1 2 3 4 5 6 7 8
B
Kb-23.1
-9.4
-6.6
-4.4
-2.3-2.0
Kb-23.1
-9.4
-6.6
-4.4
1 2 3 4 5 6 7 8 9
FIG. 5. Restriction enzyme analysis of selected group A strains.(A) Autoradiogram of EcoRI digests. Lanes: 1, 356s; 2, 365s; 3,378u; 4, 368s; 5, 364s; 6, 369s; 7, HCMV Towne DNA; 8, HFFDNA. (B) Autoradiograph of HindIII digests. Lanes: 1, 312u; 2,356s; 3, 365s; 4, 378u; 5, 368s; 6, 364s; 7, 369s; 8, HCMV TowneDNA; 9, HFF DNA.
supported by detection of similar restriction fragment pat-terns. Horizontal transmission ofHCMVs among children ingroup day-care centers has been documented in prior UnitedStates studies (1).However, a-sequence amplification alone may not com-
pletely distinguish HCMV strains. One isolate (356s), cate-gorized as a group A strain, had a restriction fragmentpattern substantially different from that of other group Astrains, an observation that indicates that additional strate-gies, such as restriction enzyme digestion of a-sequenceproducts (22) or amplification with other PCR primers (16),may be necessary to establish strain relatedness. We alsoobserved that a-sequence amplification of some isolates didnot consistently yield products, and we suspect that suchisolates possess nucleotide variations within the a sequence.In vitro selection or alteration of the a sequence duringpassage could potentially affect strain characterization. Ob-servations regarding the Towne strain indicate that the asequence remains stable through repeated passage (13),whereas the AD169 strain may be unstable (21).
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PCR ANALYSIS OF ACQUIRED HCMV INFECTIONS 2437
A10 20 30 40 50
311U aacagacACGCGTCTTCgxTTTCGCCGTGCGCGCCGCACGtCGCTTTTA
FATHER ttccttcaacagaaACGCGTCTTCgcTTTCGCCGTGtGCGCCGaACGtCGCTTTTA
TOWNE ACGCGTCTTC-TTTTCGCCGTGCGCGCCGCACGCCGCTTTTA
60 70 80 90 100 110
311U TtCGCCGtCGCCGgctTCCgCg-ACCGCcgtCcCtAcCGCaccACaCCgcaccgcAGc
FATHER TtCGCCGtCGCCGgctTCCgCg-ACCGCcgtCcCtAcCGCatcACaCCgcaccgcAGcTOWNE TGCGCCGCCGCCG---TCC-C-AACCGCAC-CGC-AACGCG--ACTCC------AAG-
120 130 140 150 160
311U ACaCgCAA-ctattcgccgtcgccgtccacacacgcaactccaat
FATHER ACaCgCAA-ctattcgccgtctccgtacacacacgcaactccatt
TOWNE ACTC-CAAA
BISOLATESANTT)Mr-'F
311U
FATHER
CGCCGCACGtCGCTTTTATtCGCCGtCGCC
CGCCGaACGtCGCTTTTATtCGCCGtCGCC
TOWNE CGCCGCACGCCGCTTTTATGCGCCGCCGCCFIG. 6. Sequence data from two HCMV isolates. (A) Comparison of a-sequence products from HCMVs isolated from child 311 and his
father. (B) Comparison of pac-2 motifs. Towne sequence data were derived from Kemble and Mocarski (11). Lowercase letters indicatedeviations from the HCMV Towne sequence. Nucleotide sequences are 5' to 3'. x, unknown.
Our results indicate that certain gene regions are con-served among clinical HCMV isolates. Primers forpp65, agene that encodes a tegument protein, and for the majorimmediate-early gene (IE-s primer) amplified most of theseHCMV strains. This result is similar to that of Zaia andcolleagues, who studied HCMV isolates from several clinicalsettings (22). However, recent data suggest that nucleotidevariations occur within exon 4 of the major immediate-earlygene, indicating that primers such as IE-s may not uniformlyamplify all HCMV isolates (6).Our data regarding the group A strains support the con-
cept that certain HCMV strains may predominate in day-care environments. In a prospective study of 104 children inday-care centers, Adler detected 14 different strains among55 HCMV-excreting children (1). However, three strainsinfected 44 of the children and were apparently transmittedwithin the day-care environment. Several factors couldaccount for this observation. Excretion of similar HCMVstrains could reflect person-to-person transmission duringclose contact (i.e., several children grouped together in oneroom) or transmission via fomites or caretakers (9). In thepresent study, group A strains were excreted by severaldifferent children in the day-care center over a period of atleast 2 years.The predominance of certain HCMV strains within a
day-care center could also reflect the intrinsic characteristicsof viral strains. The PCR data suggest that there are genomicdifferences in the a-sequence region among groups ofHCMV strains. Although analysis with restriction enzymes
has not identified biological differences among strains (19),variations in the HCMV genome may be important. Certainstrains could differ in their replicative efficiencies, a featurethat may influence viral titers in urine or saliva. Much of thepac-2 motif was conserved in the two isolates studied here,but the significance of the nucleotide variations within theremainder of the amplified a-sequence products is uncertain.Our results indicate that children in group day-care cen-
ters can be reinfected with newHCMV strains. Two childrenin the present study excreted two strains with distincta-sequence groupings. One child (311) first excreted HCMVin saliva in 1986. He subsequently had several negativesaliva cultures and one positive urine culture in 1987. He wasfound to excrete HCMV in urine in 1989, coincident withexcretion of HCMV by his younger brother and his father,who had viral hepatitis. We do not know whether child 311acquired the new strain from his sibling, other children in thecenter, or, conceivably, his father, but we are intrigued bythe observation that his second isolate was a group A strain,the predominant HCMV pattern.
Several studies of diverse human populations suggest thatreinfection with HCMV occurs. Chandler and colleaguesidentified women who either shed multiple strains ofHCMVsimultaneously from different sites or had different HCMVstrains detected during serial sampling (5). A similar phe-nomenon has been observed with homosexual men withAIDS (17). Our data and the results of Adler (2) regardingHCMV reinfection of children in day-care centers have
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substantial relevance to the biology of HCMV infections inhosts without high-risk sexual behaviors or AIDS.
ACKNOWLEDGMENTS
This work was supported by NIH grants HD22136 and HD19937and by grants from the Deafness Research Foundation and TheChildren's Miracle Network Telethon.We thank Mark Stinski for his advice and review of the manu-
script and Inara Souza for assistance with the restriction enzymedigestion of PCR products.
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