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Volume 18, Number 5—May 2012
Research
Characterization of Virulent West Nile Virus Kunjin Strain, Australia, 2011
Melinda J. Frost1, Jing Zhang1, Judith H. Edmonds1, Natalie A. Prow1, Xingnian Gu, Rodney Davis, Christine Hornitzky, Kathleen E. Arzey, Deborah Finlaison, Paul Hick, Andrew Read, Jody Hobson-Peters, Fiona J. May, Stephen L. Doggett, John Haniotis, Richard C. Russell, Roy A. Hall2, Alexander A. Khromykh2, and Peter D. Kirkland2
Table 1
Primers used for viral RNA amplification and genomic sequencing of WNV isolates from horses and mosquitoes, 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.
- Page created: April 12, 2012
- Page last updated: April 12, 2012
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