Representative mutations found in randomly

Treatment	Amplicon	Mutation
AZT Treated	HV2	11A 24A 64T 80A 128C – 382A – 396C 181A 198G 295A 320A – 345A 369A – 382C – 388A 369A – 388A 382A – 396C 388A
	CO2	7830G 7918T – 7966T – 8117T 7982C 7982C– 8019T 7985T 7986G
	ND1	3573A – 3632A – 3670A 3905G 3993C
Non-AZT Treated	HV2	79C 181A 186A-253A-296C 238A 295A 320A – 345A 331A 345A 388A
	CO2	7718A 7931C – 7982C 7985T 8087G 8206T
	ND1	3847G 3941A 3947A 4001T

Each line is a different sample. Instances of more than one mutation in a sequence are indicated by a hyphen between mutations.

Table 3: Representative mutations found in randomly selected treated and untreated samples with signature shifts for all three amplicons.

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