Volume 17, Number 2—February 2011
Dispatch
Usefulness of Published PCR Primers in Detecting Human Rhinovirus Infection
Cassandra E. Faux, Katherine E. Arden, Stephen B. Lambert, Michael D. Nissen, Terry M. Nolan, Anne B. Chang, Theo P. Sloots, and Ian M. Mackay
Table A1
Results from RT-PCR with 10 different primer pairs, targeting HRVs by using a panel of 57 clinical nucleic acid extracts from combined nose and throat swabs, Melbourne, Australia
| Specimen no. |
Species |
HRV identifier† |
Primer pairs |
||||||||||
| Original‡ (5) |
1§ (7) |
2 (8) |
3 (5) |
4 (9) |
5¶ (10) |
6 (11) |
7 (12) |
8 (13) |
9 (14) |
10 (15) |
|||
| 1 | HRV-A | HGD and MC1202 | + | + | + | + | + | 39.1 | – | – | + | – | – |
| 2 | HRV-C | PUMCH2516 | – | – | – | – | + | – | – | – | – | – | – |
| 3 | HRV-A | MC1202 | + | + | + | + | + | 33.9 | 32.7 | + | + | – | + |
| 4 | HRV-A | HRV-78 | + | + | - | + | + | 37.8 | 36.2 | – | – | + | – |
| 5 | HRV-A | HRV-80 | – | + | + | + | + | 35.1 | 33.2 | + | – | + | + |
| 6 | HRV-A | HRV-54 | – | + | + | + | + | 38.1 | 40.3 | – | + | – | + |
| 7 | HRV-B | HRV-92 | – | + | + | + | + | 32.0 | 30.7 | + | + | + | – |
| 8 | HRV-B | PUMCH2910 | + | + | + | + | + | 34.9 | 32.2 | – | + | – | – |
| 9 | HRV-B | HRV-6# | – | + | + | – | – | – | – | – | + | – | – |
| 10 | HRV-B | PUMCH5056 | – | + | + | + | + | 29.4 | 27.5 | + | + | + | – |
| 11 | HRV-B | HRV-6 | + | - | + | + | + | 40.0 | 39.9 | – | – | – | – |
| 12 | HRV-C | NH363 | + | + | + | + | + | 38.3 | 39.0 | + | + | – | – |
| 13 | HRV-C | CL-170085 | + | + | + | + | + | 35.7 | 32.6 | + | – | + | + |
| 14 | HRV-C | N33 | + | + | + | + | + | 35.2 | 32.49 | + | – | + | + |
| 15 | HRV-C | W11 | + | + | + | + | + | – | – | – | – | – | – |
| 16 | HRV-C | A98128507 | + | + | + | + | + | – | – | + | + | – | – |
| 17 | HRV-C | A99038140 | + | + | + | + | + | 37.8 | 33.5 | – | + | + | + |
| 18 | HRV-C | HRV-N10 | + | + | + | + | – | – | – | – | – | – | – |
| 19 | HRV-C | HRV-QCE** | – | + | - | + | + | 35.7 | – | – | + | – | – |
| 20 | HRV-C | W18 | + | + | + | – | – | – | – | – | – | – | – |
| 21 | HRV-C | N42 | + | + | + | + | + | 41.1 | 34.7 | + | + | – | – |
| 22 | HRV-C | CL-1237693 | + | + | - | – | – | – | – | – | – | – | – |
| 23 | HRV-C | NH4443 | + | + | + | + | + | 39.8 | – | + | + | – | – |
| 24 | HRV-C | HRV-QCE | – | + | + | + | + | 33.8 | 23.9 | + | + | + | + |
| 25 | HRV-C | W30 | + | + | – | + | + | – | 37.9 | – | – | – | – |
| 26 | HRV-C | KR2031 | – | – | + | + | - | – | – | – | – | – | – |
| 27 | HRV-C | SO4302 | – | + | + | + | + | 30.1 | 28.6 | + | + | + | – |
| 28 | HRV-C | RV1051 | – | + | + | + | + | 31.3 | 29.9 | + | + | + | + |
| 29 | HRV-C | N46 | + | + | + | + | + | 23.7 | 18.9 | + | + | + | + |
| 30 | HEV-B | HEV-97 | + | + | – | – | – | – | – | – | – | – | – |
| 31 | HEV-B | CV-B3 | – | + | – | + | + | – | 38.2 | – | – | – | – |
| 32 | HEV-A/ HRV-C | CV-A16 and W18†† | + | +‡‡ | -§§ | – | – | – | – | – | + | – | – |
| 33 | PV | UT | – | – | – | – | + | – | – | – | – | – | – |
| 34 | PV | UT | + | – | + | + | - | – | 38.8 | – | – | – | – |
| 35 | PV | UT | + | – | – | + | + | – | 41.7 | – | – | – | – |
| 36 | PV | UT | – | – | + | – | – | – | – | – | – | – | – |
| 37 | PV | UT | – | – | – | – | – | 39.6 | 37.6 | – | – | – | – |
| 38 | PV | UT | + | – | + | – | – | – | – | – | – | – | – |
| 39–41 | PV | NA | + | – | – | – | – | – | – | – | – | – | – |
| 42–56 | Neg | NA | – | – | – | – | – | – | – | – | – | – | – |
| 57 | Neg | NA | – | – | – | – | – | – | 43.4 | – | – | – | – |
| Total positive | 26 | 29 | 27 | 28 | 27 | 21 | 23 | 14 | 18 | 11 | 9 | ||
| % of all specimens | 46 | 51 | 47 | 49 | 47 | 37 | 40 | 25 | 32 | 19 | 16 | ||
*RT-PCR, reverse transcription PCR; HRV, human rhinovirus; HEV, human enter0virus, HGD, human genomic DNA; PV, member of the family Picornaviridae of unknown type; CV, coxsackievirus; UT, untypeable; neg, negative; NA, typing not attempted because there was no PCR product; +, detected; –, not detected,
†Based on best match returned by comparison of the clinical specimen's HRV sequence, derived from the amplicon, to the GenBank database.
‡Primer pair originally used and described elsewhere (1) to screen these specimens. Repeated here as primer pair 3.
§Amplicon from these primers was most commonly used to identify the HRV type and to assign a species.
¶This real-time RT-PCR was used to test the extracts during evaluation and at the end of the evaluation; steady threshold cycle values indicated that, for 5′ UTR at least, the extracted RNA had not deteriorated during the testing process. Numbers are cycle threshold values.
#Sequence identity suggested a novel HRV-B type.
**Sequence identity suggested a novel HRV-C type.
††Two distinct virus sequences determined only after amplicon cloning and direct bacterial colony PCR screening and nucleotide sequencing.
‡‡Undiscriminated positive before cloning.
§§Indicates negative for either virus.
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