1
Table S2 : Primers for the whole genome sequencing of H1N1pdm viruses
2
WHO refers to primers designed by the WHO (http://www.who.int/csr/resources/publications/swineflu/sequencing_primers/en/)
3
Virpath refers to primers designed by the laboratory
4
Segment
Forward Primer
Sequence
PB2
WHO: PB2_FOR1
WHO: PB2_FOR713
WHO: PB2_FOR1447
TGTAAAACGACGGCCAGTCTCGAGCAAAAGCAGGT
CAA
TGTAAAACGACGGCCAGTCAAGCAGTRTRTACATTG
AAGT
TGTAAAACGACGGCCAGTCCAAGYACMGAGATGTC
AATGAGA
WHO: PB1_FOR22
WHO: PB1_FOR711
WHO: PB1_FOR1489
TGTAAAACGACGGCCAGTAGCAAAAGCAGGCAAAC
CAT
TGTAAAACGACGGCCAGTTGAACACRATGACCAARG
A
TGTAAAACGACGGCCAGTATGAGYAAAAAGAAGTCY
TA
22-60
WHO: PA_FOR-0
TGTAAAACGACGGCCAGTAGCAAAAGCAGGTACTGA
T
TGTAAAACGACGGCCAGTAAATTRAGCATTGARGAY
CCG
TGTAAAACGACGGCCAGTAATGCATCCTGTGCAGCA
ATGGA
0-37
TGTAAAACGACGGCCAGTATACGACTAGCAAAAGCA
GGGG
TGTAAAACGACGGCCAGTAGRATGRACTATTACTGG
AC
1-40
PB1
PA
WHO: PA_FOR894
WHO: PA_FOR1444
HA
WHO : HA-FOR-1
WHO: HA-FOR736
5
Positio
n
1-38
713753
14471489
711748
14891527
894933
14441485
736774
Reverse Primer
Sequence
Position
WHO :PB2_REV- CAGGAAACAGCTATGACCGCTTTGRTCAAYATCRTCATT
816
WHO: PB2_REV- CAGGAAACAGCTATGACCGGAGTATTCATCYACACCCAT
1509
WHO: PB2_REV- CAGGAAACAGCTATGACCTAGTAGAAACAAGGTCGTT
2341
777-816
WHO: PB1_REV- CAGGAAACAGCTATGACCGTTCAAGCTTTTCRCAWATG
843
WHO: PB1_REV- CAGGAAACAGCTATGACCAGCTCCATGCTRAAATTRGC
1566
WHO: PB1_REV- CAGGAAACAGCTATGACCAGTAGAAACAAGGCATTT
2321
805-843
WHO : PA_REV989
WHO: PA_REV1662
WHO: PA_REV2233
CAGGAAACAGCTATGACCGGTTCTTTCCATCCAAAGAAT
GTT
CAGGAAACAGCTATGACCTCWAGTCTYGGGTCAGTGAG
947-989
CAGGAAACAGCTATGACCAGTAGAAACAAGGTACCTTTT
2194-2233
WHO : HA-REV943
WHO: HA-REV1778
CAGGAAACAGCTATGACCGAAAKGGGAGRCTGGTGTTT
A
CAGGAAACAGCTATGACCGTGTCAGTAGAAACAAGGGT
GTTT
904-943
1470-1509
2304-2341
1528-1566
2285-2321
1624-1662
1736-1778
NP
Virpath : NP-ForEsp3I
TTCGTCTCAGGGAGCAAAAGCAGGGTAGAT
1-30
Virpath : NP-RevEsp3I
ATATCGTCTCGTATTAGTAGAAACAAGGGTATTTTT
1529-1565
NA
WHO : NA-FOR-0
TGTAAAACGACGGCCAGTAGCAAAAGCAGGAGT
0-33
CAGGAAACAGCTATGACCGGRCCATCGGTCATTATG
704-740
WHO: NA-FOR726
TGTAAAACGACGGCCAGTAATGGRCARGCCTCRTAC
AA
726764
WHO : NA-REV740
WHO: NA-REV1452
CAGGAAACAGCTATGACCAGTAGAAACAAGGAG
1419-1452
M
Virpath : M_ForEsp3I
TATTCGTCTCAGGGAGCAAAAGCAGGTAG
1-29
Virpath M_RevEsp3I
ATATCGTCTCGTATTAGTAGAAACAAGGTAGTTTTT
991-1027
NS
Virpath NS_ForEsp3I
TATTCGTCTCAGGGAGCAAAAGCAGGGTG
1-29
Virpath NS_RevEsp3I
ATATCGTCTCGTATTAGTAGAAACAAGGGTGTTTT
855-890