Table 3.

Mean pairwise nucleotide distances between genotype D subgenotypes and Kenyan complete genome genotype D sequences

		Genotype D subgenotypea
		D1	D2	D3	D4	D5	D6	D-E
Genotype D full genome sequences	ELD401	0.0612	0.0648	0.0613	0.0534	0.0688	0.0494	0.0488
	ELD416	0.0405	0.0443	0.0382	0.0315	0.0467	0.0302	0.0329
	ELD422	0.0430	0.0481	0.0425	0.0332	0.0512	0.0317	0.0333
	ELD428	0.0543	0.0577	0.0535	0.0452	0.0612	0.0412	0.0423
	ELD429	0.0412	0.0450	0.0389	0.0322	0.0474	0.0308	0.0335
	KN109	0.0505	0.0534	0.0514	0.0445	0.0586	0.0389	0.0467

^aGenBank reference sequences used were as follows: D1 (AF280817, AJ344116, AF151735, GU456684, AB104711), D2 (AY090453, X72702, GQ477453, JF754597, AB078032), D3 (U95551, AY233296, AJ627217, EU921419, AB493846), D4 (HQ700500, AB033559, AB048703, FJ692533, HE974378), D5 (GQ205377, GQ205385, GQ205389, AB033558, GQ205382), D6 (FJ904409, FJ904447, FJ904403, FJ904433, FJ904438, FJ904410, FJ904395, FJ904442, KF170740, JQ927384), D-E recombinant (FN594771, FN594769, FN594770); values in bold represent nucleotide diversity >4 %