Table 1.

Positively correlated pairs of NNRTI-selected mutations

			Occurrencesb			Associationc
Mutation X	Mutation Y	Covariation within EFV/NVP subsetsa	XY	X only	Y only	P
Y181C	G190A	EFV	848	1711	985	1.8E-90
K101E	G190A	EFV, NVP	445	347	1367	3.6E-75
Y181C	H221Y	EFV, NVP	430	2105	264	7.2E-56
V108I	H221Y	EFV, NVP	255	743	430	5.4E-46
L100I	K103N	EFV	571	48	4910	6.7E-44
V108I	Y181C	NVP	424	589	2116	2.2E-32
V106A	F227L	NVP	96	66	128	1.7E-31
K101E	Y181C	EFV	351	444	2258	3.4E-28
K101E	G190S	EFV, NVP	133	672	194	1.6E-26
K103N	P225H	EFV	301	5118	30	1.2E-21
K101H	G190A	NVP	116	58	1766	2.4E-18
K103S	G190A	NVP	117	76	1753	1.2E-17
A98G	Y181C	EFV	319	617	2311	2.3E-14
V106I	Y188L	EFV	110	705	579	1.1E-11
K103N	K238T	NVP	219	5245	69	5.1E-11
K101H	Y181C		91	84	2573	5.2E-9
A98G	V108I		139	791	887	1.1E-8
G190A	H221Y		174	1671	524	1.2E-8
A98G	G190A		215	731	1657	3.3E-8
G190A	F227L		79	1797	144	1.0E-7
V108I	G190A		221	798	1606	3.4E-7
V106M	V179D	EFV	37	122	567	4.5E-7
K101E	V108I		116	679	912	6.4E-7
Y181C	G190S	EFV	120	2547	224	5.8E-6
K101P	K103S		24	207	175	1.5E-5
V108I	F227L		46	980	175	2.1E-5
H221Y	F227L		37	673	186	3.3E-5
V179F	Y181C		25	1	2648	8.3E-5
K102N	G190A		26	21	1868	1.8E-4

^aIndicates whether the pair of mutations also covaried significantly (uncorrected P < 0.05) within the subsets of sequences from individuals experienced in efavirenz (EFV) or nevirapine (NVP).

^bOccurrences in 13 039 sequences comprising the full dataset; only one isolate per patient was included in the analysis and sequences with mixtures at a given position were excluded from comparisons at that position. XY, isolates containing both mutations; X only, isolates containing mutation X but not mutation Y; Y only, isolates containing mutation Y but not mutation X.

^cP values are uncorrected values from the Jaccard covariation analysis. All mutation pairs shown above have correlations that are significant, with a Holm’s correction for multiple pairwise comparisons at P < 0.05.