TABLE 4

Parameter estimates, dN/dS, log likelihood (ℓ), and positive selection sites for RSV-A sequence data from Kilifi, Kenya

Genotype and modeldN/dSaParameter estimatesPositively selected sitesbLog likelihood (ℓ)
GA2 and ON1
    M00.655ω = 0.655None−3,681.07
    M1a0.603p0 = 0.502, p1 = 0.498; ω0 = 0.21, ω1 = 1.00Not allowed−3,661.87
    M2a0.691p0 = 0.496, p1 = 0.48, p2 = 0.03; ω0 = ,0.23 ω1 = 1.00, ω2 = 3.67274L−3,656.22
    M30.712p0 = 0.57, p1 = 0.41, p2 = 0.02; ω0 = 0.27, ω1 = 1.15, ω2 = 4.02101F, 104L, 106G, 115L, 147T, 225V, 237D, 244R, 248L, 250S, 273N, 274L, 275S, 286L (ON1: 310), 289P (ON1: 313)−3,661.99
GA5
    M00.547ω = 0.547None−1,261.92
    M1a0.547p0 = 0.99, p1 = 0.01; ω0 = 0, ω1 = 1Not allowed−1,261.92
    M2a0.547p0 = 1.00, p1 = 0.00, p2 = 0.00; ω0 = 0.55, ω1 = 1.00, ω2 = 1.00None−1,261.92
    M30.547p0 = 0.08, p1 = 0.92, p2 = 0.00; ω0 = 0.00, ω1 = 0.55, ω2 = 19.09None−1,261.92
  • a This dN/dS ratio is an average over all sites in the RSV-A alignment.

  • b The positively selected sites indicated in boldface are posterior probabilities >0.99. The positions are relative to the RSV-A reference strain (M74568).