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. 2016 Apr 29;9:247. doi: 10.1186/s13104-016-2040-4

Table 1.

Real-time PCR assays for bacteria, viruses and Streptococcus pneumoniae serotypes

Target Forward primer Reverse primer Probe (all with MGB excepta) Ref.
S. pneumoniae acgcaatctagcagatga agca tcgtgcgttttaattccagct tgccgaaaacgcttgatacagggaga [19]
H. influenzae ggttaaatatgccgatggtgttg tgcatctttacgcacggtgta ttgtgtacactccgttggtaaaagaacttgcaca [19]
A. otitidis ctacgcatttcaccgctacac ggggaagaacacggatagga agtccgccagtttccaatgccgttccaa [10]b
H. pylori cgtggcaagcatgatccat gggtatgcacggttacgagttt tcaggaaacatcgcttcaatacccactta [27]
M. catarrhalis gtcaaacagctggaggtattgc gacatgatgctcacctgctcta atcgcaattgcaacttt [28]
C. pneumoniae cgcgaaggaccttacctgga gtatctgtccttgcggaaagct ctacagttgtcaaatacatgtc [20]
M. pneumoniae cgtggtgaagtgaaacatctcagtag gcaagccctacaacccctatcta atgataagtttggcctgttc [20]
B. pertussis catcaagcaccgctttaccc tgttgggagttctggtaggtgtg cttaccgcccacagac [20]
B. parapertussis gatatcaacgggtgacggatc gcctgcacgttgctcgat cagcaattggctgcagg [20]
SP serotype 1 cgtgcggtaattgaagctatga tgtggccccagcaactct cttgcccttgtatagggt [21]
SP serotype 3 ggtcagcagaaagtatgcattgg tcgtttatccagggtctgatga tattggatgtggtttatcgtgaag [21]
SP serotype 4 cggcaggcaaaccaattat catctcgttcgggactaaca caggagatgctaaaata [21]
SP serotype 5 ttacgggagtatcttatgtctttaatgg cagcattccagtagcctaaaactaga tctcagcaactctatttgg [21]
SP serotype 6A gctagagatggttccttcagttgat catactctagtgcaaactttgcaaaat ctggctcatgatagtt [21]
SP serotype 6B gctagagatggttccttcagttgat catactctagtgcaaactttgcaaaat actgtctcatgataatt [21]
SP serotype 7F/A aagcacagtgcgtgaacaat aaaatctccctgtcccttcc ctattccagaagaatctc [21]
SP serotype 9 V/A tggaatgggcaaagggtagta tcggttccccaagattttctc ttaatcatgctaacggctcat [21]
SP serotype 14 cgactgaaatgtcactaggagaagat aatacagtccatcaattactgcaatactc attcgtttgccaatacttga [21]
SP serotype 18C/B ccctgaaactagttgggaaca ttccaatcatcacccattaca aaagtcagatgttaaagactac [21]
SP serotype 19A gctgtgtttatgggggttgg agagacgtttaggctcatttgc atgcaaaatgctcacctag [21]
SP serotype 19F/B/C aattcggtatttatgggagttgg agagacgtttaggctcattagc atgcaaaagtcaaatttaga [21]
SP serotype 23F ctgggccaagatatttaaaagagagt aattccgcatcagagtatgcaa ttgctcttcgaaaaatgt [21]
RSV A ctcaatttcctcacttctccagtgt cttgattcctcggtgtacctctgt cattatgcctaggccagcag [20]
RSV B ttcctaacttctcaagtgtggtccta ctggtttcttggcgtacctctatac tcccattatgcctagacct [20]
Influenza A ccccctcaaagccgagat caagattggtcttgtctttagcca ccatgagagcctcaagat [20]
Influenza B aatacggtggattaaacaaaagcaa caggaggtctatatttggttccatt catattgggcaatttccta [20
HMPV A cacctgagtgatttatcatacaagca ttagcatacagaatttctccacacaa acaccctcatcattgc [20] MGB
HMPV B caagaacaaatgtgacattgctgat gaaaactgccgcacaacatttag aagctgacagccatct [20]
Rhinovirus caagtaatggacagggtgtgaagag ccaaagtagtcggtcccatcc tccggcccctgaat [20]
Enterovirus gcccctgaatgcggctaa ggaaacacggacacccaaagta tctgcagcggaacc [20]
Bocavirus ggcagaattcagccatactcaaa tctgggttagtgcaaaccatga ccacagtcatcagacact [20] MGB
Adenovirus ccacggtggggtttctaaactt cccagtggtcttacatgcacatc tgcaccagacccgg [20]
Coronavirus OC43 cgatgaggctattccgactaggt ccttcctgagccttcaatatagtaacc tccgcctggcacggt [20]
Coronavirus 229E ttccgacgtgctcgaacttt ccaacacggttgtgacagtga tcctgaggtcaatgca [20]
Coronavirus HKU1 gccttgcgaatgaatgtgct tgcatcaccactgctagtaccac ttgctattatgttaagcctg [20] MGB
Coronavirus NL63 ggaagcgtgttcctaccagaga agcaagctgtggaaaacctttg caaagcactgaataac [20]
PIV1 acagatgaaattttcaagtgctactttagt gcctcttttaatgccatattatcattaga atggtaataaatcgactcgct [20]
PIV 2 tgcatgttttataactactgatcttgctaa gttcgagcaaaatggattatggt actgtcttcaatggagatat [20]
PIV 3 tgctgttcgatgccaacaa attttatgctcctatctagtggaagaca ttgctcttgctcctca [20]
PIV 4 cctggagtcccatccaaagtaag tgagactgttattttaagtgcatctatacg tttgttgatcaagacaatac [20]

RSV Respiratory syncytial virus; PIV Parainfluenza virus; HMPV human metapneumovirus; SP S. pneumoniae

a Probes contained an internal quencher and no minor groove binder. All other probes contained a minor groove binder and no internal quencher

b Primers from published reference, probe this study