Molecular Characterization of Newcastle Disease Virus from Backyard Poultry Farms and Live Bird Markets in Kenya

Table 3

Mean evolutionary distance between the complete nucleotide sequences of the fusion gene of the study sample, NDVs of genotype V, and the LaSota strain.

Evolutionary distance^1
Genotype	SS	Vd	Vb	Vc	Va	II
SS	—	[0.005]	[0.010]	[0.010]	[0.012]	[0.018]
Vd^2	0.031	—	[0.009]	[0.008]	[0.011]	[0.017]
Vb	0.126	0.112	—	[0.005]	[0.007]	[0.015]
Vc	0.105	0.093	0.070	—	[0.007]	[0.014]
Va	0.142	0.127	0.099	0.090	—	[0.017]
II	0.235	0.224	0.213	0.186	0.224	—
Vd (with SS)	—	—	[0.009]	[0.008]	[0.10]	[0.017]
Vb	—	0.115	—	[0.005]	[0.007]	[0.015]
Vc	—	0.097	0.069	—	[0.006]	[0.014]
Va	—	0.130	0.099	0.089	—	[0.016]
II	—	0.226	0.213	0.186	0.224	—

¹The number of base substitutions per site obtained by averaging all sequence pairs between subgenotypes of genotypes V and II (which are the common vaccine strains). The first half shows the evolutionary distance estimates obtained when the study sample (KE1007/2016: MG988405) is not included in subgenotype Vd, and the second half shows evolutionary distances when the study sample is included in subgenotype Vd. In total, 59 sequences were used: subgenotype Vd (n = 5), Vb (n = 12), Vc (n = 9), Va (n = 15), genotype II (n = 11), and the study sample. Values in square brackets are standard errors calculated by the bootstrap method (1000 replicates). Analysis was conducted using maximum composite likelihood analysis in MEGA 6. A total of 1662 positions were in the final dataset. ²Previous NDVs from Uganda classified under a new subgenotype Vd [32].