Table 1.
Primers used for reverse transcription, PCR and sequencing
| RT | Sequence 5′‐3′ | Sequencing | Sequences 5′‐3′ |
|---|---|---|---|
| 2.06neg | tttagtaaaaagaccacc | 0.67+ | cctaaggattacgctgatgcttttgc |
| 4.26neg | catacttttgcgcatc | 1.26+ | ttcgcaggaacttgtcttgcaagc |
| 6.18neg | agaaaacctacaccag | 2.52+ | tagaggaatgtcacagcttggtgc |
| 8.18neg | gtaaagaatgtactaaac | 3.04+ | tacaccaatgtcacagcttggtgc |
| 10.10neg | cacagttgtgtgcactaactcaaag | 3.10+ | ctctcgatgttgtgaatttaccatctgg |
| 12.10neg | ctccataagaatcctg | IB4.6+a | gtacggatgaagtaatagaagcttc |
| 14.13neg | taaaacttggttgttcc | 4.80+ | tgattgtgatgttgtgaatttaccatctgg |
| 16.10neg | ttcacataaagcatcaac | IB5.15nega | catcagtatcaggtgttaacttataag |
| QX18.10neg | catagaagaagaatggcatagctttc | 5.32+ | ctattagtcttagggcaatatggg |
| 19.73neg | caaaatgcattactcgc | IB5.70+a | gtgtggtttatttacacaagtaatccag |
| 22.51neg | catatcttctttttgacc | 6.53+ | gttaaacctacagcatatgcttacc |
| 24.08neg | tttgaatcattaaacagac | IB6.7nega | ctaatcgttctgaaagtgcctgatcaag |
| 26.24neg | ccaagatacatttccag | IB7.15+a | ctttataacaagatctggtgctaaac |
| 27.89neg | Ttgctctaactctatac | 7.17+ | aatgctcctccggtagtatggaag |
| Dta‐Adaptnegb | gcatctcgaggcttgtggcttttttttttttttttttttta | IB8.2nega | caacccaaactagcattattgtaaacac |
| Dtc‐Adaptnegb | gcatctcgaggcttgtggctttttttttttttttttttttc | 8.60+ | gtatgatggcaacgagtttgttgg |
| Dtg‐Adaptnegb | gcatctcgaggcttgtggctttttttttttttttttttttg | IB8.61nega | taccaacaaactcgttgccatc |
| PCR | Sequence 5′‐3′ | 9.26+ | cctgtcactatgcgttctaatggtac |
| 0.06+ | gcgctagatttccaacttaacaaaacg | 10.60+ | ggtaaatccacctaaaactgtgtggg |
| 2.03neg | gacttgcgaaacaagatgccaaatgcc | 11.13+ | gaagttagatagcatggagagacg |
| 1.92+ | tggaggcttgcatatggaaaagtgcg | 12.64+ | gacttaaagtcagaagtaacagctg |
| 4.20neg | ggtataaagaggatttctttatcctcaagatcatg | 13.18+ | gatctcctcaagtatgattatactgagg |
| 4,10+ | cggaggatggtgttaaataccgc | QX13.90+ | gaggtgacgtctaaatattttgaatg |
| 6.08neg | caaataatattagaaagaccaaataaagccaattcc | 14.69+ | caaggtcttgtagcagatatttctgg |
| 5.90+a | gactatggtaaagactcatttgacg | 15.25+ | aagtgttgctatgaccatgtcatgc |
| 8.05neg | cctggtttagtatactcacatacactacc | IB15.60+a | ggtgcagcttggtgattttacctttg |
| 7.97+ | cctaatggtgttaggcttatagttcc | IB16.40nega | ctataaccttgaaacactgacgtg |
| 10.10neg | gtactaaagactacaggatcataccattg | QX16.80neg | gaatcagctgtaacacagaatataac |
| 10.02+ | cagttattattggagtttgtgctgaag | 16.62+ | catgaaagtggctcagcctacaac |
| 12.08neg | gaatcctgatccggagttggacttggc | 17.18+ | caacatgttttataacacgtgatgaggc |
| 12.01+ | gtggcagcaggtaatcaacctttagg | 18.02neg | ctgcttgacattgggtactactggattc |
| 14.12neg | ataaaacttggttgttccaataactacagg | 18.18+ | taacctacctggttgtaatggtgg |
| 14.05+ | gtgtctatcctttctactatgactaataggc | 18.71+ | gaagagaaatattcgcacactgcc |
| 16.09neg | cacataaagcatcaacagctgcatgag | 19.67nega | gtattgacagagttgtgtatactttggc |
| QX15.06+ | gatgattgcactcgcatagtacctc | 19.46+ | gtaacagtgtcaattgattaccatagc |
| QX18.10neg | catagaagaagaatggcatagctttc | 19.97+ | gatagccaataatggcaatgatgacg |
| 17.62+a | tactcaggcttatgcttgttggaagc | IB20.40+a | cattgtttatagtgtctcttttgtttgcac |
| 19.67neg | gtattgacagagttgtgtatactttgcc | IB21.70nega | gtcacaaattgcccttatgtaagttatgg |
| 19.46+ | gtaacagtgtcaattgattaccatagc | IB21.95+a | ccagcagtttgtagtttctggtgg |
| 22.26neg | tccatacgcgtttgtatgtactcatctg | IB23.60nega | cacgtgcagtgatgtagtaactacc |
| IB21.95+ | ccagcagtttgtagtttctggtgg | QX24.20neg | ctacttacactgtttcaattgttttctc |
| IB24.07neg | gaatcattaaacagactttttaggtctg | IB24.70+a | gtactcttggtactgaacaagcag |
| 23.99+ | cattatgcctctaatgagtaagtgtgg | IB25.60nega | ctcttgaaaagagagcatgaaacaaagagg |
| 26.24nega | ccaagatacatttccag | QX27.20a,b | cctacatgtctatcgccaggg |
| 26.02+ | gaaaagcgcgaatttatctgagagaagg | ||
| 27.83neg | catagccaattaaacttaacttaaactaaaatttagctc | ||
| 26.49+ | gatagccaagatggtatagtgtggg | ||
| Adapt negb | gcatctcgagggttgtggc |
Primer names generally indicate approximate binding positions in the 624I genome.
Coding and anticoding sense primers are labelled + and neg, respectively.
aIndicates primers designed for the 624I IBV strain sequencing based on the newly determined flanking sequences. bIndicates primers used for the retrotranscription, amplification, and sequencing of the 3′END of the genome.
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