Table 2 Additional PCRs for SIV testing of a subset of samples (n = 4).
Primers tested | Primer sequences | Estimated amplicon size | Region targeted | Reference |
|---|---|---|---|---|
DR1-DR2/DR4-DR5 | DR1 (5'-TRCAYACAGGRGCWGAYGA-3') | 800 | Pol | [44] |
DR2 (5'-AIADRTCATCCATRTAYTG -3') | ||||
DR4 (5'-GGIATWCCICAYCCDGCAGG-3') | 200 | |||
DR5 (5'-GGIGAYCCYTTCCAYCCYTGHGG -3') | ||||
polOR-polis4/polis2uni2 | polOR(5'-ACBACYGCNCCTTCHCCTTTC -3') | 800 | Pol | [10] |
polis4(5'-CCAGCNCACAAAGGNATAGGAGG-3') | ||||
polis2(5'-TGGCARATRGAYTGYACNCAYNTRGAA-3') | 650 | |||
uni2(5'-CCCCTATTCCTCCCCTTCTTTTAAAA -3') | ||||
wrcpol | wrcpolF1 (5'-TAGGGACAGAAAGTATAGTAATHTGG-3') | 1100 | Pol | [25] |
wrcpolR1 (5'-GCCATWGCYAA TGCTGTTTC-3') | ||||
wrcpolF2 (5'AGAGACAGTAAGGAAGGGAAAGCAGG-3') | 650 | |||
wrcpolR2 (5'-GTTCWATTCCTAACCACCAGCADA-3') | ||||
wrcenv | wrcenvF1 (5'-TGGC AGTGGGACAAAAATATAAAC-3') | 750 | Env | [25] |
wrcenvR1 (5'-CTGGCAGTCCCTCTTCCA AGTT GT-3') | ||||
wrcenvF2 (5'TGATAGGGMTGGCTCCTGGTGATG3') | 550 | |||
wrcenvR2 (5'-AATCCCCATTTYAACCAGTTCCA-3') | ||||
wrcgag | wrcgagF1 (5'-ATDGAGGATAGAGGNTTTGGAGC-3') | 600 | Gag | [46] |
wrcgagR1 (5'-GCCCTCCTACTCCTTGACATGC-3') | ||||
wrcgagF2 (5'-CCAACAGGGTCAGATATAGCAG-3') | 250 | |||
wrcgagR2 (5'-ACTTCTGGGGCTCCTTGTTCTGCTC-3') | ||||
olcpol | olcpolF1(5-TAGATACAGGRGCAGATGAYACAGTAAT-3') | 700 | Pol | S. Locatelli, unpublished data |
olcpolR1 (5'TCCAYCCYTGAGGHARYACATTATA-3') | ||||
olcpolF2 (5'-CTAGAATWATWGGRGGRATAGGRGG-3') | 300 | |||
olcpolR2 (5'-ATYTTWCCTTCTKCTTCYARTCTRTCACA-3') | ||||
bwcpol | bwcpolF1 (5'-TAGATACAGGAGCAGATGATACAGT-3') | 1000 | pol | S. Locatelli, unpublished data |
bwcpolR1 (5'-ATTDCCYCCTATCCCTTTATGWGC-3') | ||||
bwcpolF2 (5'-AGAYTRGAAGCAGARGGAAAAAT-3') | 600 | |||
bwcpolR2 (5'-TCCYACCAATTTYTGTAYATCATTTACTGT-3') | ||||
polis4-SIVenvR/lhoenv | polis4(5'-CCAGCNCACAAAGGNATAGGAGG-3') | 3600 | Env | [47] |
SIVENVR (5'-YTBYTGCTGCTGCAMTATCCC-3') | ||||
lhoenvF2 (5'- AATCAGATAGTNYAGCAAGCATGG-3') | 600 | |||
lhoenvR2 (5'-CCATTAAAKCCAAAGAAGCTACT-3') | ||||
polis4/PolOr polF2/polR2 | polOR(5'-ACBACYGCNCCTTCHCCTTTC -3') | 800 | Pol | [48] |
polis4(5'-CCAGCNCACAAAGGNATAGGAGG-3') | ||||
POLF2 (GGAAGTGGATACTTAGAAGCAGAAGT-3') | 330 | [5] | ||
POLR2 (5'-CCCAATCCCCCCTTTTCTTTTAAAATT-3') | ||||
gp40F1-gp41R1 gp46F2/gp48R2 | gp40F1(5'-TCTTAGGAGCAGCAGGAAGCACTATGGG-3') | 850 | Env | [49] |
gp41R1(5'- AACGACAAAGGTGAGTATCCCTGCCTAA-3') | ||||
gp46F2(5'-ACAATTATTGTCTGGTATAGTGCAACAGCA-3') | 445 | |||
gp48R2(5'-TCCTACTATCATTATGAATATTTTTATATA-3') | ||||
SPBS-wrcgagR1/SPBS-wrcgagR2 | SPBS (5'-GGCGCCCGAACAGGGACTTG-3') | 1500 | LTR-gag | M. Peeters, unpublished data |
smmgag | smmgagF1 (5'-TGGGAGATGGGCGCGAGAAACTCCGTC-3') | 1000 | gag | [50] |
smmgagR1 (5'-ATCAGCAGTGTCTGTGTCATCCAATT-3') | ||||
smmgagF2 (5'-AGGGAAAAAAGCAGATGAATTAGAA--3') | 800 | |||
smmgagR2 (5'-GCTCTTGTAGAAYCTATCTACATA-3') | ||||
smmenv (gp41) | smmenvF1 (5'-GCTACGGCAGGTTCTGCAATGGG-3') | 650 | env | [50] |
smmenvR1 (5'-CTGGTCCTTGCGGATATGGATCTG-3') | ||||
smmenvF2 (5'-GCTGTCCGCTCAGTCCCGGACTTT-3') | 490 | |||
smmenvR2 (5'-GGAGGAGAACACTGGCCTATA-3') |