Does antiretroviral treatment change HIV-1 codon usage patterns in its genes: a preliminary bioinformatics study

Palanisamy, Navaneethan; Osman, Nathan; Ohnona, Frédéric; Xu, Hong-Tao; Brenner, Bluma; Mesplède, Thibault; Wainberg, Mark A.

doi:10.1186/s12981-016-0130-y

AIDS Research and Therapy

Table 1 Codon usage in pol and gag genes of HIV-1 in treatment-naive and treatment-experienced individuals

From: Does antiretroviral treatment change HIV-1 codon usage patterns in its genes: a preliminary bioinformatics study

Amino acid	Codon	pol			gag
Amino acid	Codon	Naive (N = 532)	Treated (N = 52)	P value	Naive (N = 524)	Treated (N = 54)	P value
Alanine	GCU	15.60 ± 0.17	13.87 ± 0.52	0.0018**	23.10 ± 0.17	23.58 ± 0.65	0.7689
	GCC	19.66 ± 0.12	20.72 ± 0.42	0.0189*	18.38 ± 0.19	18.49 ± 0.58	0.9689
	GCA	63.25 ± 0.12	63.72 ± 0.34	0.1477	49.08 ± 0.22	48.46 ± 0.61	0.5766
	GCG	1.48 ± 0.07	1.68 ± 0.20	0.0932	9.43 ± 0.12	9.47 ± 0.40	0.7388
Arginine	CGU	0.09 ± 0.02	0.14 ± 0.08	0.3506	0.15 ± 0.03	0.20 ± 0.12	0.6272
	CGC	0.06 ± 0.02	0.05 ± 0.05	0.7593	0.23 ± 0.04	0.19 ± 0.11	0.8865
	CGA	3.33 ± 0.07	3.04 ± 0.15	0.2125	3.03 ± 0.10	3.30 ± 0.35	0.4781
	CGG	3.09 ± 0.05	3.41 ± 0.20	0.0621	5.58 ± 0.10	6.02 ± 0.33	0.2211
	AGA	60.65 ± 0.27	63.90 ± 0.72	0.0002***	56.80 ± 0.26	57.27 ± 0.78	0.5734
	AGG	32.77 ± 0.27	29.47 ± 0.71	0.0001***	34.20 ± 0.27	33.01 ± 0.90	0.0845
Asparagine	AAU	74.66 ± 0.25	76.56 ± 0.59	0.0189*	62.61 ± 0.34	63.48 ± 0.89	0.4616
Asparagine	AAC	25.34 ± 0.25	23.44 ± 0.59	0.0189*	37.39 ± 0.34	36.52 ± 0.89	0.4616
Aspartic acid	GAU	59.40 ± 0.21	60.58 ± 0.59	0.1349	47.57 ± 0.40	49.08 ± 1.31	0.1854
Aspartic acid	GAC	40.60 ± 0.21	39.42 ± 0.59	0.1349	52.43 ± 0.40	50.92 ± 1.31	0.1854
Cysteine	UGU	86.81 ± 0.33	86.76 ± 1.05	0.8285	80.66 ± 0.56	81.56 ± 1.45	0.8737
Cysteine	UGC	13.19 ± 0.33	13.24 ± 1.05	0.8285	19.34 ± 0.56	18.44 ± 1.45	0.8737
Glutamic acid	GAA	72.48 ± 0.16	73.05 ± 0.62	0.2699	65.35 ± 0.27	66.64 ± 0.82	0.1509
Glutamic acid	GAG	27.52 ± 0.16	26.95 ± 0.62	0.2699	34.65 ± 0.27	33.36 ± 0.82	0.1509
Glutamine	CAA	59.33 ± 0.15	59.62 ± 0.63	0.4549	59.93 ± 0.33	55.65 ± 1.05	0.0006***
Glutamine	CAG	40.67 ± 0.15	40.38 ± 0.63	0.4549	40.07 ± 0.33	44.35 ± 1.05	0.0006***
Glycine	GGU	10.21 ± 0.08	11.24 ± 0.24	0.0001***	2.52 ± 0.11	3.16 ± 0.40	0.2888
	GGC	5.42 ± 0.10	5.45 ± 0.27	0.9708	21.22 ± 0.16	20.00 ± 0.52	0.0279*
	GGA	54.09 ± 0.15	54.47 ± 0.51	0.5641	46.95 ± 0.28	48.74 ± 0.72	0.0483*
	GGG	30.28 ± 0.16	28.84 ± 0.54	0.0076**	29.31 ± 0.23	28.10 ± 0.67	0.0936
Histidine	CAU	67.75 ± 0.35	70.96 ± 1.00	0.0043**	59.17 ± 0.56	63.59 ± 1.92	0.0136*
Histidine	CAC	32.25 ± 0.35	29.04 ± 1.00	0.0043**	40.83 ± 0.56	36.41 ± 1.92	0.0136*
Isoleucine	AUU	29.95 ± 0.11	30.74 ± 0.30	0.0073**	23.52 ± 0.25	22.33 ± 0.79	0.1297
	AUC	15.23 ± 0.09	14.46 ± 0.29	0.0325*	15.73 ± 0.25	19.56 ± 0.82	<0.0001***
	AUA	54.82 ± 0.08	54.80 ± 0.29	0.9037	60.75 ± 0.20	58.10 ± 0.81	0.0003***
Leucine	UUA	39.10 ± 0.14	39.49 ± 0.51	0.5880	44.21 ± 0.23	42.06 ± 0.79	0.0027**
	UUG	10.72 ± 0.11	10.75 ± 0.33	0.8305	13.01 ± 0.14	12.63 ± 0.43	0.6161
	CUU	12.19 ± 0.12	11.78 ± 0.32	0.1110	12.48 ± 0.15	12.01 ± 0.41	0.2454
	CUC	6.62 ± 0.06	6.30 ± 0.24	0.1421	10.57 ± 0.11	10.52 ± 0.38	0.9979
	CUA	19.65 ± 0.17	18.96 ± 0.48	0.2819	12.12 ± 0.25	15.19 ± 0.67	<0.0001***
	CUG	11.72 ± 0.11	12.71 ± 0.30	0.0054**	7.62 ± 0.13	7.59 ± 0.50	0.7665
Lysine	AAA	72.28 ± 0.14	72.47 ± 0.39	0.6021	66.80 ± 0.23	66.78 ± 0.72	0.9256
Lysine	AAG	27.72 ± 0.14	27.53 ± 0.39	0.6021	33.20 ± 0.23	33.22 ± 0.72	0.9256
Phenylalanine	UUU	65.69 ± 0.19	66.09 ± 0.71	0.5312	61.11 ± 0.36	58.32 ± 1.28	0.0214*
Phenylalanine	UUC	34.31 ± 0.19	33.91 ± 0.71	0.5312	38.89 ± 0.36	41.68 ± 1.28	0.0214*
Proline	CCU	26.08 ± 0.13	26.53 ± 0.35	0.1652	29.76 ± 0.18	28.69 ± 0.61	0.1140
	CCC	18.13 ± 0.13	18.04 ± 0.40	0.8455	14.29 ± 0.17	13.69 ± 0.69	0.1897
	CCA	54.53 ± 0.10	54.64 ± 0.32	0.7969	52.49 ± 0.18	54.31 ± 0.73	0.0072**
	CCG	1.25 ± 0.07	0.80 ± 0.16	0.0330*	3.46 ± 0.13	3.32 ± 0.48	0.3902
Serine	UCU	6.62 ± 0.12	6.64 ± 0.33	0.9876	2.01 ± 0.11	3.38 ± 0.43	0.0005***
	UCC	3.41 ± 0.09	3.39 ± 0.31	0.7542	11.96 ± 0.14	12.59 ± 0.47	0.2148
	UCA	26.98 ± 0.14	26.83 ± 0.53	0.9924	32.96 ± 0.20	32.27 ± 0.73	0.7226
	UCG	0.77 ± 0.06	1.12 ± 0.21	0.0563	0.89 ± 0.09	1.28 ± 0.36	0.4649
	AGU	39.58 ± 0.23	39.35 ± 0.79	0.6742	15.17 ± 0.22	14.56 ± 0.71	0.3236
	AGC	22.63 ± 0.17	22.67 ± 0.52	0.7640	37.02 ± 0.24	35.91 ± 0.90	0.3998
Threonine	ACU	30.57 ± 0.12	30.39 ± 0.44	0.4910	25.24 ± 0.20	25.23 ± 0.62	0.8150
	ACC	13.88 ± 0.10	13.28 ± 0.36	0.1156	28.67 ± 0.20	28.53 ± 0.85	0.5475
	ACA	54.44 ± 0.11	55.11 ± 0.40	0.0659	44.77 ± 0.20	45.10 ± 0.73	0.8720
	ACG	1.11 ± 0.06	1.23 ± 0.19	0.6161	1.32 ± 0.10	1.14 ± 0.33	0.4743
Tyrosine	UAU	69.25 ± 0.17	68.61 ± 0.61	0.3502	86.34 ± 0.41	83.80 ± 1.47	0.2448
Tyrosine	UAC	30.75 ± 0.17	31.39 ± 0.61	0.3502	13.66 ± 0.41	16.20 ± 1.47	0.2448
Valine	GUU	15.04 ± 0.11	15.57 ± 0.34	0.1411	10.46 ± 0.20	11.03 ± 0.57	0.4377
	GUC	12.87 ± 0.10	12.85 ± 0.32	0.9003	9.38 ± 0.19	8.56 ± 0.62	0.1446
	GUA	58.66 ± 0.14	57.82 ± 0.37	0.0379*	57.59 ± 0.30	57.85 ± 0.99	0.5363
	GUG	13.43 ± 0.12	13.76 ± 0.36	0.2377	22.58 ± 0.25	22.57 ± 0.82	0.8879

Values are given as mean ± SEM in %. p values <0.05*, <0.01**, and <0.001***

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