Table 1. PCR assays used in the study.
| Virus | Reagents; cycles; primers (sequence 5′-3′) | Target region | Amplicon length [base pairs] | Reference |
| Lassa | OneStep RT-PCR kit (Qiagen); 45 cycles; 36E2 (ACCGGGGATCCTAGGCATTT), LVS-339-rev (GTTCTTTGTGCAGGAMAGGGGCATKGTCAT) | 5′UTR/GPC gene | 320 | [24] |
| RVF | OneStep RT-PCR kit (Qiagen); 45 cycles; RVS (AAAGGAACAATGGACTCTGGTCA), RVAs (CACTTCTTACTACCATGTCCTCCAAT) | G2 gene | 95 | [25] |
| Flavia | OneStep RT-PCR (Qiagen); 45 cycles; VD8 (GGGTCTCCTCTAACCTCTAG), EMF1 (TGGATGACSACKGARGAYATG) | NS5/3′UTR | 500–700 | [26] |
| CCHF | OneStep RT-PCR kit (Qiagen); 45 cycles; CC1a_for (GTGCCACTGATGATGCACAAAAGGATTCCATCT), CC1b_for (GTGCCACTGATGATGCACAAAAGGATTCTATCT), CC1c_for (GTGCCACTGATGATGCACAAAAGGACTCCATCT), CC1a_rev (GTGTTTGCATTGACACGGAAACCTATGTC), CC1b_rev (GTGTTTGCATTGACACGGAAGCCTATGTC), CC1c_rev (GTGTTTGCATTGACACGGAAACCTATATC) | N gene | 280 | [28] |
| CCHF | OneStep RT-PCR kit (Qiagen); 45 cycles; RWCF (CAAGGGGTACCAAGAAAATGAAGAAGGC), RWCR (GCCACAGGGATTGTTCCAAAGCAGAC) | N gene | 180 | [27] |
| Filob | OneStep RT-PCR kit (Qiagen); 45 cycles; FiloA2.2 (AAGCCTTTCCTAGCAACATGATGGT), FiloA2.3 (AAGCATTCCCTAGCAACATGATGGT), FiloA2.4 (AAGCATTTCCTAGCAATATGATGGT), Filo B (ATGTGGTGGGTTATAATAATCACTGACATG), Filo B-Ra (GTGAGGAGGGCTATAAAAGTCACTGACATG) | L gene | 290 | [29] |
| HBV | Platinum Taq polymerase (Invitrogen); 40 cycles; HBV-2263(+) (TTCGGAGTGTGGATTCGCACTCCT), HBV-2958(−) (GTTGGGATTGAAGTCCCAATCTGGAT) | P gene | 730 | [30] |
| HEV | First-round: Superscript II One Step RT-PCR kit (Invitrogen); 40 cycles; HE040 (CCCTTRTCCTGCTGAGCRTTCTC), HE044 (CAAGGHTGGCGYTCKGTTGAGAC); Nested: Platinum Taq polymerase (Invitrogen); 25 cycles; HE110-2 (mixture of GYTCKGTTGAGACCTCYGGGGT, GYTCKGTTGAGACCACGGGYGT, GYTCKGTTGAGACCTCTGGTGT), HE041 (TTMACWGTCRGCTCGCCATTGGC) | ORF2 | 460 | [31] |
| HEV | First-round: Superscript II One Step RT-PCR kit (Invitrogen); 35 cycles; HE361 (GCRGTGGTTTCTGGGGTGAC), HE364 (CTGGGMYTGGTCDCGCCAAG); Nested: Platinum Taq polymerase (Invitrogen); 25 cycles; HE363 (GMYTGGTCDCGCCAAGHGGA), HE366 (GYTGATTCTCAGCCCTTCGC) | ORF2/ORF3 | 140 | [32] |
| HAV | OneStep RT-PCR kit (Qiagen); 40 cycles; 2870 (GACAGATTCTACATTTGGATTGG), 3381 (CCATTTCAAGAGTCCACACACT) | VP1/2A junction | 510 | [33], [34] |
| HCV | OneStep RT-PCR kit (Qiagen); 45 cycles; Pr3 (TATGAYACCCGCTGYTTTGACTC), Pr4 (GCNGARTAYCTVGTCATAGCCTC) | NS5B | 380 | [35] |
a
Flaviviruses including YF and dengue virus.
b
Filoviruses including Ebola and Marburg virus.