TABLE 4.

Summary of synonymous and nonsynonymous nucleotide substitutions in rep and cap

IsolateSubstitutionsa
cap HVR (400 bp)cap non-HVR (1,800 bp)3′ rep (600 bp)
snss/nsRate/ntsnss/nsRate/ntsnss/nsRate/nt
LG1520111.87.55769.53.5942.32.1
S1748580.825.892910.25.61125.52.3
T1717101.76.662415.53.7732.31.4
T3217101.76.662415.53.7632.01.2
T4012101.25.454318.03.2933.01.9
T411581.95.647411.82.8431.31.1
T701061.73.94868.03.01744.32.6
T711581.95.647411.82.8331.00.9
T881892.06.645592.81343.32.4
Avg ± SD1.6 ± 0.278.2 ± 3.9b12.1 ± 2.8c3.5 ± 0.62.8 ± 1.11.8 ± 0.6
  • a s is the number of observed synonymous substitutions in the indicated coding region; ns is the number of observed nonsynonymous substitutions in the indicated coding region; s/ns is the calculated ratio. The rate/nt value represents the number of observed nucleotide substitutions per 100 bp of sequence.

  • b Substitution rate in HVR region was greater than that observed for non-HVR and 3′ rep region, P = 0.04 and 0.02, respectively, using paired t test.

  • c Ds/Da ratio in non-HVR region was greater than that observed for HVR and 3′ rep region, P = 0.00002 and 0.0001, respectively, using paired t test.