Whole genome sequencing of SIV-infected macaques identifies candidate loci that may contribute to host control of virus replication

Table 1 Animals used for whole genome sequencing

Designation		ID	MHC	GZMB	52 week viral load (log10)	Sex	Number of reads mapped	Reference
Cohort A	Group 1	cy0321	M1/M1	G1/G5	1.7	M	1222977688	[9]
		cy0322	M1/M1	G1/G4	1.9	M	1093240092	[9]
		cy0323	M1/M1	G1/G3	2.0	M	1161761415	[9]
		cy0326	M1/M3	G1/G4	2.5	M	1014048607	[9]
		cy0327	M1/M3	G1/G5	2.0	M	1158978497	[9]
		cy0330	M1/M3	G3/G6	2.9	M	1120820126	[9]
	Group 2	cy0320	M1/M1	G4/G4	5.9	M	1210339744	[9]
		cy0324	M1/M1	G4/G4	5.7	M	1192434815	[9]
		cy0325	M1/M1	G2/G3	6.8	M	1091870521	[9]
		cy0328	M1/M3	G4/G4	6.3	M	1356197360	[9]
		cy0329	M1/M3	G2/G3	6.7	M	1169431587	[9]
		cy0331	M1/M3	G4/G5	5.5	M	1314518723	[9]
Outgroup		cy0332	M3/M3	G2/G4	6.1	M	1206633787	[9]
		cy0333	M3/M3	G3/G5	6.5	M	1217425129	[9]
		cy0334	M3/M3	G2/G5	5.0	M	1094844832	[9]
		cy0335	M3/M3	G1/G4	5.0	M	1298840412	[9]
		cy0336	M3/M3	G2/G5	6.2	M	1244446132	[9]
		cy0337	M3/M3	G3/G4	6.0	M	1357235243	[9]

Whole genome sequencing was performed on 18 SIV-infected Mauritian cynomolgus macaques. For each animal, the MHC genotype, GZMB genotype, 52 week viral load (log₁₀ viral RNA copies per milliliter of plasma), sex, and number of sequencing reads mapped to rheMac2 are shown for the 12 Cohort A M1(+) animals, and an outgroup of 6 M3/M3 macaques.

ISSN: 1474-760X