Analysis of infectious virus clones from two HIV-1 superinfection cases suggests that the primary strains have lower fitness

Table 2 Characteristics and results of the competition experiments of selected biological clones

Clone no.	*Ex vivo*competition results ^a	Replication remarks	LTR	Tat	CCR5/CXCR4 use ^b
Patient L
B1.1	Against B2.3: lose	B1.1 and B1.2 replicate at similar level ex vivo	16 and 13 nt insertions	T23N and F32L mutations	CCR5
	Against B2.5: lose
B1.2	Against B2.3: lose		n.d.	n.d.	CCR5
	Against B2.5: lose
B1.3	Against B2.3: lose	B1.3 replicates at a lower level than B1.1 and B1.2 ex vivo.	16 and 13 nt insertions	T23N and F32L mutations	CCR5
	Against B2.5: lose
B2.3	Against B1.1: win		Destabilizing mutation in TAR hairpin		CCR5
	Against B1.2: win
	Against B1.3: win	B2.3 and B2.5 replicate at similar level ex vivo
B2.5	Against B1.1: win		n.d.		CCR5
	Against B1.2: win
	Against B1.3: win
Patient P
B3.1	Against B4.1: win	B3.1 replicates at very low levels in vivo	Destabilizing mutation in poly A hairpin	Short variant (86 aa)	CXCR4
	Against B4.2: win
	Against B4.3: lose
	Against B4.4: lose
B4.1	Against B3.1: lose				CCR5
B4.2	Against B3.1: lose				CCR5
B4.3	Against B3.1: win	B4.3 and B4.4 replicate at similar level ex vivo			CCR5
B4.4	Against B3.1: win				CCR5

^a Primary clones of patient L (B1.1, B1.2 and B1.3) were competed against the superinfecting clones B2.3 and B2.5. For patient P, primary clone B3.1 was competed against all four B4 clones.
^b As predicted by the Geno2pheno coreceptor prediction algorithm [70]. Additionally, clone B3.1 grows in MT2 cultures, again suggestive of CXCR4 use.

ISSN: 1742-4690