Table 1 Sequences and target regions of the primers used in the identification of CHIKV isolates
Virus or genus | Gene target | Primer sequence | Position | References | |
|---|---|---|---|---|---|
1 | Flavivirus | NS5 | FU 1; (5ʹ-TAC AAC ATG ATG GGA AAG AGA GAG AA-3ʹ) | 9007–9032 | [18] |
NS5 | CFD2; (5ʹ-GTG TCC CAG CCG GCG GTG TCA TCA GC-3ʹ) | 9308–9283 | |||
2 | Bunyavirus | Nucleocapsid protein | BCS82C; (5ʹ-ATG ACT GAG TTG GAG TTT CAT GAT GTC GC-3ʹ) | 86–114 | [19] |
Nucleocapsid protein | BCS332V; (5ʹ-TGT TCC TGT TGC CAG GAA AAT-3ʹ) | 309–329 | |||
3 | Alphavirus | NSP4 | VIR 2052F; (5ʹ-TGG CGC TAT GAT GAA ATC TGG AAT GTT-3ʹ) | 6917–6997 | [20] |
NSP4 | VIR 2052R; (5ʹ-TAC GAT GTT GTC GTC GCC GAT GAA3ʹ) | 7086–7109 | |||
4 | Ndumu | Envelope (E1) gene | ND 124F; (5ʹ-CAC CCT AAA AGT GAC GTT-3ʹ) | 124–141 | [18] |
Envelope (E1) gene | ND 615R; (5ʹ-ATT GCA GAT GGG ATA CCG-3ʹ) | 615–632 | |||
5 | Babanki | E1 envelope glycoprotein | Bab 3368F; (5ʹ-CAG CAG ATT GCG CGA CTG ACC-3ʹ) | 3368–3388 | [18] |
E1 envelope glycoprotein | Bab 4203R; (5ʹ-GCT CAC GAT ATG GTC AGC AGG-3ʹ) | 4184–4203 | |||
6 | Sindbis | Nonstructural protein | SINV1; (5ʹ-TTT AGC GGA TCG GAC AAT TC-3ʹ) | 5194–5213 | [18] |
Nonstructural protein | SINV2; (5ʹ-GCG GTG ACG AAC TCA GTA G-3ʹ) | 6482–6500 | |||
7 | Chikungunya | Capsid gene | CHIK 7028F; (5ʹ-TGC GCG GCC TTC ATC GGC GAC TAC-3ʹ) | [21] | |
CHIK 8288r; (5ʹ-CCA GGT CAC CAC CGA GAG GG-3ʹ) |