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Volume 17, Number 5—May 2011

Research

Evolution of New Genotype of West Nile Virus in North America

Allison R. McMullen, Fiona J. May, Li Li, Hilda Guzman, Rudy Bueno, James A. Dennett, Robert B. Tesh, and Alan D.T. BarrettComments to Author 
Author affiliations: Author affiliations: University of Texas Medical Branch, Galveston, Texas, USA (A.R. McMullen, F.J. May, L. Li, H. Guzman, R.B. Tesh, A.D.T. Barrett); Harris County Public Health and Environmental Services, Houston, Texas, USA (R. Bueno, Jr., J.A. Dennett)

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Table 4

Positive and negative selection results for West Nile virus isolates, Upper Texas Gulf Coast, USA, 2002–2009*

Protein Amino acid residues relative to ORF Length of protein, aa Overall dN/dS Single-likelihood ancestor counting†

Fixed effects
likelihood†

Internal fixed effects likelihood†
Positive selection Negative selection Positive selection Negative selection Positive selection Negative selection
ORF 1–3,333‡ 3,333 0.110 2 246 8 619 16 25
C 1–123 123 0.270 0 2 0 9 0 2
prM 124–290 166 0.134 0 7 0 25 1 3
E 291–791 500 0.119 0 15 1 72 1 3
NS1 792–1143 351 0.134 0 17 1 48 4 4
NS2A 1144–1374 230 0.130 0 15 1 48 1 3
NS2B 1375–1505 130 0.118 0 6 0 19 0 1
NS3 1506–2124 618 0.083 0 42 0 101 0 6
NS4A 2125–2273 148 0.135 0 7 1 22 0 3
NS4B 2274–2522 248 0.112 0 13 0 49 0 8
NS5 2529–3433 904 0.098 0 61 2 148 4 10

*ORF, open reading frame; dN, nonsynonymous nucleotide substitutions; dS, synonymous nucleotide substitutions; C, capsid; prM, premembrane; E, envelope; NS, nonstructural.
†No. sites where p<0.1.
‡Only the first 3,333 aa residues of the ORF were used for these analyses because of program constraints on alignment size.

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