Table 2.

Classification of CLSs detection according to primate lentiviral families

	HIV-1		HIV-2		AGM		Macaques		Sooty M.		CPZ.		Mandrill		Sykes' monkey
MMy 1	●a	PBS – U5b	●	PBS – U5	●	PBS	●	PBS	●	PBS	●	PBS	●	PBS
MMy 3	●	gag (p17)	●	gag	●	gag	●	gag	●	gag	●	gag	■	gag
MMy $4^{\prime }$	●	gag (p24)	●	gag	■	gag – pol	●	gag	●	gag	■	gag / pol
MMy 28	●	gag (p7)	●	gag			■	gag	■	gag	■	gag / pol
MMy 31	●	pol (p15)	●	pol	●	pol	●	pol	●	pol	●	pol / vif	●	pol	●	pol
MMy 32	●	pol (p31)	●	pol	●	pol	●	pol	●	pol	●	vif	●	pol	●	vif
CLS 1	●	pol (p31) /	●	pol / vpr	●	pol / pol	●	pol	●	pol / env	●	pol	●	pol / vif
		pol (p31)
CLS 2	●	pol (p31) / nef	●	pol / nef	■	nef	■	nef	●	nef	●	pol / nef	●	pol / nef	●	vif
CLS 3	●	gag (p6) –	■	pol	●	pol	■	pol	●	pol	●	pol	■	pol	●	pol
		pol (p10)
CLS 4	●	gag (p24)	●	gag / env	■	gag	●	gag	●	gag	■	gag / vpr	●	gag
CLS 5	●	gag (p24)	●	gag	■	gag	■	gag	■	gag	●	gag	■	gag
CLS 6	●	pol (p31)	●	pol	●	pol	●	pol	●	pol	●	pol / vif	●	pol
CLS 7	●	nef / U3									■	LTR / nef / pol
CLS 8	●	pol (p51)							■	pol	●	pol
CLS 9	●	pol (p51)									●	pol
CLS 10	●	gag (p17) /	○	env					■	env	●	pol	■	pol
		pol (p51)
CLS 11	●	pol (p31) /									●	pol	●	pol
		env (gp120–V3)
CLS 12	●	pol (p51)									■	pol	■	pol
CLS 13	●	pol (p31) /
		env (gp120–V4)
CLS 14	■c	gag (p17) / vpu
CLS 15	■	pol (p31)									■	pol
CLS 16	●	pol (p31)	■	pol	■	pol	■	pol	■	pol	■	pol / env	■	pol	●	vif
CLS 17	○	vif	●	env	■	rev	■	env	■	tat – rev – env
CLS 18			●	gag / gag / pol	●	gag / gag	●	gag / gag	■	gag			■	gag
CLS 19			■	gag			●	gag	■	gag
CLS 20			●	env			●	env	●	env
CLS 21			●	vpx			●	vpx	●	vpx
CLS 22					●	env							■	gag	●	tat

^aDetection degree of the tested CLS in the genomes: (●) at least 90%; (■) comprised between 10% and 89%; (○) less than 10%.

^bGene location of the CLSs: genes separated by ( / ) when CLS was detected on each of the two genes; genes separated by (–) when CLS overlapped the 2 genes; gene indicated in italics when CLS was present at an occasional position.

^cA gradual detection of CLS 14 was observed when the admitted transitions in this sequence varied from 1 (66%) to 7 (85%).