Volume 18, Number 5—May 2012
Characterization of Virulent West Nile Virus Kunjin Strain, Australia, 2011
|RT-PCR region||Forward primer, 5′ → 3′ (relative genome position†)||Reverse primer, 5′ → 3′ (relative genome position†)|
|Amplification and sequencing of whole genome|
|5′ NTR capsid||TAGTTCGCCTGTGTGAGCTG (5′ NTR-2)||TTGAAAATTCCACAGGAATGG (capsid-1772)|
|Capsid-NS2A||GTGATAGCATTGGGCTCWCA (capsid-1720)||ATCTTGAAGGYYGCCATGAG (NS2A-1760)|
|NS2A-NS3||CACTGATGTGTTACGCTATGTCA (NS2A-3678)||CAAAGTCCCAATCATCGTTCT (NS3-5807)|
|NS3-NS5||CGGTTTGGTTTGTGCCTAGT (NS3-5687)||CCAACTTCACGCAGGATGTA (NS5-9235)|
|NS5–3′ NTR||GACCACTGGCTTGGAAGAAA (NS5-9169)||CTGGTTGTGCAGAGCAGAAG (3′ NTR-10955)|
|Partial sequencing of key regions of genome|
|NS3||GTGCTGGTAAAACAAGGAGG (NS3-5201)||TGTATCCTCTAGCCGCGATG (NS3-5493)|
|NS5||TCGGCCCAGATGATGTG (NS5-9575)||CGGCATGGAACCACCAGTGTTC (NS5-9860)|
*Primers were designed from available sequences in GenBank to cover the coding regions of any WNV genome. WNV, West Nile virus; RT, reverse transcription; NTR, nontranslated region; NS, nonstructural protein.
†WNVNY99 GenBank accession no. NC_009942.1.
1These authors contributed equally to the major technical aspects of this research.
2These authors served as joint senior authors.
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