Successes have been reported with RNAi technology using either single or multiple viral gene sequences, or by artificial miRNA [ 27- 29].
Phylogenetic analyses of 396 additional HIV env sequences (8), together with those from the ISLA method, revealed multiple additional identical viral sequences (8), strongly suggesting that multiple HIV-infected clonal cell populations persist during ART (Fig. 2 and figs. S2 and S3).
GOS psbA viral sequences formed multiple coherent clusters containing predominantly Synechococcus myoviral sequences, Prochlorococcus myoviral sequences, or those from uncultured environmental viruses (Fig. 2A).
It is notable that analysis of a relatively large and unbiased sample of viral sequences from multiple seasons with straightforward molecular evolutionary methods yields this unexpectedly complex picture of virus evolution.
However, due to the lack of such reference sequences, identification of HIV-1 intrasubtype recombinants has been limited to cases in which known sequences of transmitted multiple viral variants could serve as references for recombination analysis [ 8].
The 423-nt VP1 3′ end fragment (nt 2912 3334, according to the EV11 polyprotein genome, X80059) was analyzed through the multiple sequence comparison of the 64 viral sequences from Spain, the EV13 and ENV69 prototype strains (Del Carmen and Toluca-1, respectively), and the isolates VA86-6776 (30 ) and TX95-2089 (7 ).
This motif is also found in some coronaviruses and equine rhinovirus serotype 2. The conservation of such a sequence motif across multiple viral families suggests that it may play a broad role in the biology of positive-stranded RNA viruses (28 ), although the exact function of this conserved region is still unknown.
We assumed that presence of recombinant sequences in the pool of viral quasispecies provides evidence for transmission of multiple viral variants, even if the source of recombination (parent sequence) has not been identified.
Each participant had identical viral sequences integrated at the same position in multiple cells, demonstrating infected-cell proliferation.
In addition to compatibility with Pol II promoters, pri-miR sequences may be multimerized to enable simultaneous silencing at multiple viral targets.
