Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations

Table 2 Amino acid heterogeneity of V3 region of HIV-1 proviral quasispecies harboured by monocytes (CD36) and T lymphocytes (CD26) and of plasma virions replicating in the two cell types after HAART interruption.

Patient	Sample type		N. of unique variants*	Diversity**	Complexity***
Pt.1	Provirus	CD36	161	0.0795 ± 0.0005	0.3798
		CD26	226	0.0197 ± 0.0001	0.2119
Pt.2	Provirus	CD36	231	0.1446 ± 0.0005	0.3620
		CD26	59	0.0031 ± 0.0001	0.0919
Pt.3	Provirus	CD36	46	0.0508 ± 0.0003	0.3042
		CD26	3	0.0084 ± 0.0002	0.0738
	Virus	CD36	26	0.0428 ± 0.0010	0.2979
		CD26	158	0.0298 ± 0.0003	0.3293
Pt.4	Provirus	CD36	76	0.0226 ± 0.0007	0.1127
		CD26	14	0.0457 ± 0.0003	0.1755
	Virus	CD36	15	0.0113 ± 0.0002	0.1138
		CD26	41	0.0208 ± 0.0002	0.1222
Pt.5	Provirus	CD36	157	0.0585 ± 0.0003	0.2756
		CD26	120	0.0411 ± 0.0004	0.4233
	Virus	CD36	305	0.0728 ± 0.0005	0.3664
		CD26	38	0.0042 ± 0.0001	0.0870

Sequences obtained by ultra-deep pyrosequencing were filtered through the correction algorithm and amino acid sequences obtained were analyzed to establish diversity and complexity, as described in the Materials and Methods section.
* Number of unique sequences obtained after dereplication
** Diversity: p distance ± SEM
*** Complexity: normalized Shannon entropy

ISSN: 1742-4690