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Background  HIV infection has been reported to alter cellular gene activity, but published studies have commonly assayed transformed cell lines and lab-adapted HIV strains, yielding inconsistent results. Here we carried out a deep RNA-Seq analysis of primary human T cells infected with the low passage HIV isolate HIV 89.6 .    Results  Seventeen percent of cellular genes showed altered activity 48 h after infection. In a meta-analysis including four other studies, our data differed from studies of HIV infection in cell lines but showed more parallels with infections of primary cells. We found a global trend toward retention of introns after infection, suggestive of a novel cellular response to infection. HIV 89.6  infection was also associated with activation of several human endogenous retroviruses (HERVs) and retrotransposons, of interest as possible novel antigens that could serve as vaccine targets. The most highly activated group of HERVs was a subset of the ERV-9. Analysis showed that activation was associated with a particular variant of ERV-9 long terminal repeats that contains an indel near the U3-R border. These data also allowed quantification of >70 splice forms of the HIV 89.6  RNA and specified the main types of chimeric HIV 89.6 -host RNAs. Comparison to over 100,000 integration site sequences from the same infected cell populations allowed quantification of authentic versus artifactual chimeric reads, showing that 5′ read-in, splicing out of HIV 89.6  from the D4 donor and 3′ read-through were the most common HIV 89.6 -host cell chimeric RNA forms.    Conclusions  Analysis of RNA abundance after infection of primary T cells with the low passage HIV 89.6  isolate disclosed multiple novel features of HIV-host interactions, notably intron retention and induction of transcription of retrotransposons and endogenous retroviruses.    Electronic supplementary material  The online version of this article (doi:10.1186/s12977-015-0205-1) contains supplementary material, which is available to authorized users.

Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats