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Research
Lineage 1 and 2 Strains of
Encephalitic West Nile Virus, Central Europe
Tamás Bakonyi,*† Éva Ivanics,‡ Károly Erdélyi,‡ Krisztina Ursu,‡ Emőke
Ferenczi,§ Herbert Weissenböck,* and Norbert Nowotny*¶
*University of Veterinary Medicine, Vienna, Austria; †Szent István University,
Budapest, Hungary; ‡Central Veterinary Institute, Budapest, Hungary; §"Béla
Johan" National Center for Epidemiology, Budapest, Hungary; and ¶United
Arab Emirates University, Al Ain, United Arab Emirates
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Appendix Table 1. Oligonucleotide
primers used for sequencing West Nile virus (WNV) strain Goose-Hungary/03*
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Name*
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Sequence 5´ to 3´
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Product length (bp)
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WNVI 1f
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AGTAGTTCGCCTGTGTGAGC
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388
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WNVI 388r
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GCCGATTGATAGCACTGGTC
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WNVI 82f
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AGCACGAAGATCTCGATGTC
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986
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WNVI 1067r
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ATGATAGTCACGCAGCTGTC
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WNVI 1005f
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AGGAGTGTCTGGAGCAACAT
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995
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WNVI 1999r
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AAGCCACTGACGAGATAGGA
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WNVI 1864f
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ACAACCTATGGCGTCTGTTC
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1,049
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WNVI 2912r
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CGATTCTGAGTCGGACATTC
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WNVI 2847f
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AGAACTCGCCAACAACACCT
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774
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WNVI 3620r
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ATCTTGGCTGTCCACCTCTT
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WNVI 3502f
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CTCGTGCAGTCACAAGTGAA
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957
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WNVI 4458r
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ATCAAGCCGCACATCAACTC
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WNVI 4524f
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GGTCTGTCTCGCGATTAGTG
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500
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WNVI 5023r
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GTGAGCCTGATGTTCCAGTG
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WNVI 5300f
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CTGAGATGGCTGAAGCACTG
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858
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WNVI 6157r
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TCTCACGCTCTGGTTGGTAG
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WNVI 5303f
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AGATGGCTGAAGCACTGAGA
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162
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WNVI 5464r
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CCATCACGAACAGGTTGTAG
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WNVI 6009f
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GTCGCAAGTTGGTGATGAGT
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228
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WNVI 6236r
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TCTGCAGTCCTCAACAGTTC
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WNVI 6119f
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ACGGACTGATCGCTCAATTC
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1,151
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WNVI 7269r
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AAGGAGTGTTGCCGCTGTTA
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WNVI 7177f
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TTCGTCGATGTTGGAGTGTC
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993
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WNVI 8169r
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CCGAATCGTCCTATGCTCTT
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WNVI 8112f
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TTGTGACATCGGAGAGTCCT
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1068
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WNVI 9179r
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AGCCAGTGGTCTTCATTGAG
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WNVI 8950f
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GCCAGAGAAGCAGTTGAAGA
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305
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WNVI 9254r
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CCAACTTCACGCAGGATGTA
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WNVI 9134f
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TTCTGGAGTTCGAGGCTCTG
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1,186
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WNVI 10319r
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CCGATGATTGCTCTGACTTG
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WNVI 9445f
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GGAAGAACCGTCATGGATGT
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466
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WNVI 9910r
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GAGCTCTGCCTACCAATTCA
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WNVI 10524f
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CGCCACCGGAAGTTGAGTAG
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501
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WNVI 11024r
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CTGTGTTCTCGCACCACCAG
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*Numbers refer to nucleic acid positions at the
5´-end of the primers, according to the complete genomic sequence
of the closely related WNV strain WN NY 2000-crow3356 (AF404756;
1). f, forward (genomic) primer; r, reverse
(complementary) primer.
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Appendix Table 2. Oligonucleotide
primers used for sequencing of West Nile virus (WNV) strain goshawk-Hungary/04
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Name*
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Sequence 5´ to 3´
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Product length (bp)
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WNVII 1f
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AGTAGTTCGCCTGTGTGAGC
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200
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WNVII 200r
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AGCATAGCCCTCTTCAGTCC
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WNVII 81f
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TGGCACGAAGATCTCGATGT
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874
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WNVII 954r
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TGCCACCAGGAGCAATAGAA
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WNVII 870f
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CCTCGTTGCAGCTGTCATTG
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761
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WNVII 1630r
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TCCATGGCAGGTTCAGATCC
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WNVII 1584f
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CTTCCTGGTTCACCGAGAAT
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908
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WNVII 2491r
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CTTGCCTGCCAATGTCAATG
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Usu 2328f
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CTCTTTGGRGGRATGTCHTG
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818
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Usu 3145r
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GTGCADGATTTKACYTCTCC
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WNVII 3027f
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CAACATGGCTGTGCATAGTG
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673
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WNVII 3699r
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GCCGACGAGAATGACATATC
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Usu 3606f
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AAGAGGTGGACGGCCARRHT
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1,152
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Usu 4759r
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GTGTGCCAYAGYGTGTGGAA
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WNVII 3861f
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GGCTTACTATGACGCCAAGA
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594
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WNVII 4454r
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CCATCATCATCCAGCCTAAC
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Usu 4251f
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ATGTTYGCCATYGTWGGDGG
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1,142
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Usu 5392r
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TGGCACATSACATCMACKAT
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WNVII 5294f
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TTGCTGCTGAGATGTCTGAG
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324
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WNVII 5617r
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TGTCCGAGATAGGAGCATTG
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Usu 5454f
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ATGGATGAAGCYCATTTCAC
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337
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Usu 5790r
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GGTAYTCYGTMTCATAGGAC
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WNVII 5629f
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GCCTGGAACACTGGATATGA
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616
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WNVII 6245r
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TAAGCGAGCCAGACTGGTAA
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WNVII 6127f
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TATCAGCCTGAGCGCGAGAA
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932
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WNVII 7058r
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ACGGCTGTCGTTACGGCATA
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WNVII 6935f
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ATGACATTGGCAGCCTGTTG
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672
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WNVII 7606r
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ATCCTCCTCGCATGATGTGA
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WNVII 7505f
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GAGAGGCTGGAATTCTGACT
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653
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WNVII 8158r
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GTTCTTCTACCTCGGCACTT
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WNV 8078f
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CATCAGAAGCGAGCGACACA
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744
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WNV 8821r
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ACAGCCAGTTCGTGGTCTCA
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WNV 8723f
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TCGGTCAACAACGAGTGTTC
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739
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WNV 9461r
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GAGATGACGTCCATCACAGT
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WNV 9368f
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TAGCGCGGTCCATCATCGAG
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733
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WNV 10100r
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CCAACGTTCGACCGGAGTCT
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WNVII 10023f
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CTGTTCCGCTGTGCCTGTCA
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519
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WNVII 10541r
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CGTGGATCACCTCGCAGCTT
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WNV 9031f
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TACAACATGATGGGVAARAGAGAGA
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1,061
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WNV 10091r
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AGCATGTCTTCYGTBGTCATCCAYT
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WNV 10460f
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GCCACCGGAAGTTGAGTAGA
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430
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WNV 10889r
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GCTGGTTGTGCAGAGCAGAA
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Usu 10596f
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GWAAGCCTCYCAGAACCGTCTCGGAAG
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419
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Usu 11014r
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AGATCCTGTGKTCTWSYYCMCCAYCAG
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*Numbers refer to nucleic acid positions at the
5´-end, according to the complete genomic sequence of the
closely related lineage 2 WNV strain B956 (NC_001563). Universal,
Japanese encephalitis virus–group specific primers are indicated
in italics (2). f, forward (genomic)
primer; r, reverse (complementary) primer. Usu, Usutu.
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Appendix
References
- Lanciotti RS, Ebel GD, Deubel V, Kerst AJ, Murri S,
Meyer R, et al. Complete
genome sequences and phylogenetic analysis of West Nile virus strains
isolated from the United States, Europe, and the Middle East. Virology.
2002;298:96–105.
- Bakonyi T, Gould EA, Kolodziejek J, Weissenbock H, Nowotny N. Complete
genome analysis and molecular characterization of Usutu virus that emerged
in Austria in 2001: comparison with the South African strain SAAR-1776
and other flaviviruses. Virology. 2004;328:301–10.
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