Table 1 Primers used to detect and to sequence arbovirus from mosquito pools in Kenya

Universal primers for flavivirus

MAMD

AACATGATGGGRAARAGRGARAA

Forward

252

94°C, 2 min, 1 cycle; 94°C, 1 min, 53°C, 1 min, 72°C, 1 min, 35 cycles; 72°C, 5 min, 1 cycle

Scaramozzino et al. (2001) [48]

cFD2

GTGTCCCAGCCGGCGGTGTCATCAGC

Reverse

Universal primers for flavivirus

FLAVI-1

AATGTACGCTGATGACACAGCTGGCTGGGACAC

Forward

854–863

94°C, 5 min, 1 cycle; 94°C, 1 min, 58°C, 1 min, 72°C, 90 s, 45 cycles; 72°C, 10 min, 1 cycle

Ayers et al.(2006) [49]

FLAVI-2

TCCAGACCTTCAGCATGTCTTCTGTTGTCATCCA

Reverse

Universal primers for flavivirus (mainly YF)

YF-1

GGTCTCCTCTAACCTCTAG

Forward

675

94°C, 2 min, 1 cycle; 94°C, 30 s, 53°C, 30 s, 72°C, 1 min, 35 cycles; 72°C, 5 min, 1 cycle

Tanaka et al. (1993) [50]

YF-3

GAGTGGATGACCACGGAAGACATGC

Reverse

Universal primers for alpha viruses (mainly chikungunya and o’nyong’nyong viruses)

nsP1-S

TAGAGCAGGAAATTGATCC

Forward

354

94°C, 2 min, 1 cycle; 94°C, 30 s, 53°C, 30 s, 72°C, 45 s, 35 cycles; 72°C, 5 min, 1 cycle

Hasebe et al. (2002) [51]

nsP1-C

CTTTAATCGCCTGGTGGTA

Reverse

Universal primers for alpha viruses (mainly chikungunya and o’nyong’nyong viruses)

E1-S

TACCCATTCATGTGGGG

Forward

294

94°C, 2 min, 1 cycle; 94°C, 30 s, 53°C, 30 s, 72°C, 45 s, 35 cycles; 72°C, 5 min, 1 cycle

Hasebe et al. (2002) [51]

E1-C

GCCTTTGTACACCACGAT

Reverse

Rift Valley virus

RVF009

CCAAATGACTACCAGTCAGC

Forward

400–500

94°C, 2 min, 1 cycle; 94°C, 30 s, 50°C, 30 s, 72°C, 1 min, 35 cycles; 72°C, 5 min, 1 cycle

Jupp et al. (2000) [52] (modified)

RVF007

GACAAATGAGTCTGGTAGCA

Reverse

Mosquito RNA marker

Act-2F

ATGGTCGGYATGGGNCAGAAGGACTC

Forward

683

94°C, 2 min, 1 cycle; 94°C, 30 s, 54°C, 30 s, 72°C, 45 s, 35 cycles; 72°C, 5 min, 1 cycle

Staley et al. (2010) [53]

Act-8R

GATTCCATACCCAGGAAGGADGG

Reverse

Culex quinquefaciatus

ACEpip

GGAAACAACGACGTATGTACT

Forward

610

94°C, 5 min, 1 cycle; 94°C, 30 s, 54°C, 30 s, 72°C, 1 min, 35 cycles; 72°C, 5 min, 1 cycle

Kasai et al. (2008) [39]

ACEquin

CCTTCTTGAATGGCTGTGGCA

Forward

274

B1246s

TGGAGCCTCCTCTTCACGG

Reverse

Aedes aegypti

18SFHIN

GTAAGCTTCCTTTGTACACACCGCCCGT

Forward

550

97°C, 4 min, 1 cycle; 96°C, 30 s, 48°C, 30 s, 72°C, 2 min, 30 cycles; 72°C, 4 min, 1 cycle

Higa et al. (2010) [54]

aeg.r1

TAACGGACACCGTTCTAGGCCCT

Reverse

Anopheles funestus, Anopheles rivulorum

UV

TGTGAACTGCAGGACACAT

Forward

94°C, 2 min, 1 cycle; 94°C, 30 s, 45°C, 30 s, 72°C, 40 s, 30 cycles; 72°C, 5 min, 1 cycle

Koekemoer et al. (2002) [55]

RIV

CAAGCCGTTCGACCCTGATT

Reverse