Volume 18, Number 5—May 2012
Research
Characterization of Virulent West Nile Virus Kunjin Strain, Australia, 2011
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.