Table 1 Primers and probes used to detect arbovirus and hepatitis E virus
Primers and probes | Nucleic acid sequences of primers and probes |
|---|---|
qPCR Zika virus (ZIKV) | |
ZIKV forward | 5-nt9271AARTACACATACCARAACAAAgTggT9297–3’ |
ZIKV reverse | 5′ nt9352-TCCRCTCCCYCTYTggTCTTg-9373 -3’ |
ZIKV probe | nt 9304-FAM-CTYAgACCAgCTgAAR-BBQ-9320 |
qPCR Dengue total (DENV 1–4 system) | |
DENT forward | 5′- AGGACYAGAGGTTAGAGGAGA - 3’ |
DENT reverse | 5′- CGYTCTGTGCCTGGAWTGAT −3’ |
DENT probe | FAM-ACAGCATATTGACGCTGGGARAGACC-TAMRA |
qPCR Dengue subtypes (DENV1, DENV2, DENV3) | |
DEN1 forward | 5′ ATACCYCCAACAGCAGGAATT - 3’ |
DEN1 reverse | 5′ AGCATRAGGAGCATGGTCAC −3’ |
DEN1 probe | FAM-TTGGCTAGATGGRGCTCATTCAAGAAGAAT-TAMRA |
DEN2 forward | 5′ TGGACCGACAAAGACAGATTCTT 3’ |
DEN2 reverse | 5′ CGYCCYTGCAGCATTCCAA 3’ |
DEN2 probe | FAM-CGCGAGAGAAACCGCGTGTCRACTGT-TAMRA |
DEN3 forward | 5′ AAGACGGGAAAACCGTCTATCAA 3’ |
DEN3 reverse | 5′ TTGAGAATCTCTTCGCCAACTG 3’ |
DEN3 probe | FAM-ATGCTGAAACGCGTGAGAAACCGTGT-TAMRA |
qPCR Chikungunya (CHIK) | |
CHIK forward | 5′- AAGCTYCGCGTCCTTTACCAAG - 3’ |
CHIK reverse | 5′- CCAAATTGTCCYGGTCTTCCT −3’ |
CHIK probe | FAM-CCAATGTCYTCMGCCTGGACACCTTT-TAMRA |
qPCR Rift Valley fever virus (RVFV) | |
RVFV forward | 5′- AAA ggA ACA ATg gAC TCT ggT CA - 3’ |
RVFV reverse | 5′- CAC TTC TTA CTA CCA TTC CTC CAA T − 3’ |
RVFV probe | FAM-AAA gCT TTg ATA TCT CTC AgT gCC CCA A -TAMRA |
qPCR West Nile virus (WNV) | |
WNV3p forward | 5′ Agg TTA gWg gAg ACC CCg T - 3’ |
WNV3p reverse | 5′ ggT TgT gCA gAg CAg AAg ATC −3’ |
WNV3p probe | FAM-CGGTTCCGGCGGTGGTTTCT-TAMRA |
Conventional PCR Crimean-Congo haemorrhagic fever virus (CCHFV) | |
CCHFV forward | 5′ – TGGACACCTTCACAAACTC - 3’ |
CCHFV reverse | 5′ – GACAAATTCCCTGCACCA - 3’ |
qPCR Hepatitis E virus (HEV) | |
HEV forward | 5′ GCCCGGTCAGCCGTCTGG −3’ |
HEV reverse | 5′-CTGAGAATCAACCCGGTCAC −3’ |
HEV probe | FAM-CGGTTCCGGCGGTGGTTTCT-TAMRA |