Table 2.

Dual Infection Per-Region Analysis

Sample	Estimated duration of infection (months)	Genetic region	SGS: dual infection?	UDS first duplicate: dual infection?	UDS second duplicate: dual infection?
A	3.1	env C2-V3	N (1.0%)	N (2.6%)	N (2.1%)
		pol RT	N (1.0%)	N (1.7%)	N (1.6%)
		gag p24	N/A	N (0.8%)	N (0.8%)
B	7.3	env C2-V3	N (0%)	N (1.7%)	N (0.8%)
		pol RT	N (0%)	N (1.6%)	N (0.8%)
		gag p24	N/A	N (0.8%)	N (1.6%)
C	1.5	env C2-V3	N (0.3%)	N (0%)	N (0.8%)
		pol RT	N (0.8%)	N/A (poor quality reads)	N/A (poor quality reads)
		gag p24	N/A	N (0%)	N (0.8%)
D1	31	env C2-V3	Y (12.5%)	Y (18%)	Y (18.4%)
		pol RT	Y (2.4%)	Y (4.1%)	Y (4.9%)
		gag p24	N/A	N (3.2%)	N (2.0%)
E	39.9	env C2-V3	N (3.4%)	N (5.9%)	N/A
		pol RT	N (2.0%)	N (4.1%)	N/A
		gag p24	N/A	N (1.6%)	N/A
F	49.6	env C2-V3	N (3.9%)	N (7.0%)	N/A
		pol RT	N (1.8%)	N (3.2%)	N/A
		gag p24	N/A	N (3.2%)	N/A
D2	33.8	env C2-V3	Y (11%)	Y (20.2%)	Y (20.4%)
		pol RT	Y (5.2%)	Y (3.3%)	Y (5.5%)
		gag p24	N/A	N (3.2%)	N (3.2%)
G	2.8	env C2-V3	N (0%)	N (0.9%)	N/A
		pol RT	N (0.4%)	N (0.8%)	N/A
		gag p24	N/A	N (0.8%)	N/A
H	70.6	env C2-V3	N (1.2%)	N (0%)	N (0%)
		pol RT	Y (4.4%)	Y (2.4%)	Y (4.0%)
		gag p24	N/A	N (0.8%)	N (0%)
I	1.5	env C2-V3	Y (16.4%)	Y (27%)	Y (27%)
		pol RT	Y (5.7%)	Y (5.8%)	Y (8.2%)
		gag p24	N/A	Y (8.2%)	Y (7.4%)

N/A: Not applicable, since gag SGS was not performed. Samples E, F, and G lacked sufficient cDNA to run UDS duplicates. Divergence values are shown in parentheses as the bootstrapped bottom 5% quantile of the divergence distribution.