High background may obscure the actual viral production. Therefore, for further analysis, we evaluated HIV-1 tissue infection by enumerating CD4 T cells positive for intracellular p24 by flow cytometry. At 12 or 15 days post-infection, the tissues were digested and stained for intracellular p24. We detected p242expressing cells in tissues following exposure to all the tested HIV-1 variants (Fig. 1). To avoid the exclusion of CD4 T cells that may have down-regulated CD4 expression as a result of HIV-1 infection, we defined CD4 T cells as CD82CD3+ cells [9]. Initially, we inoculated tissue from three 22948146 donors in parallel with the T/F variant NL-1051.TD12.ecto and the C/R variant NLSF162.ecto. We found no statistical difference between the fractions of CD4 T cells infected by these viruses (inhibitor Autophagy respectively 14.1264 and 17.7465.9 , n = 3, p = 0.74). Neither were there statistically significant differences (p = 0.08) between the fractions of p242expressing CD4 T cells in the group of tissues infected with the C/R HIV-1 as compared to the group of tissues infected with T/F HIV-1. On average, the p24+ CD4 T cell fraction in C/ R HIV-1 infected tissues constituted 12.661.5 (median 12.6 , IQR [7.61 ?7.1 ] n = 19) of total CD4 T cells, while in tissues infected with T/F viruses this fraction constituted 8.2562.6 (median 3.76 , IQR [0.96 ?5.8 ], n = 14) (Fig. 1). Next, we estimated the depletion of CD4 T cells by comparing the ratio of CD8+ to CD4+ T cells (i.e. CD82CD3+) in infected and uninfected controls [5,8,10]. To pool data obtained from different donors, we normalized the data by expressing the CD4/ CD8 ratio in infected tissue as a percent of the same ratio in matched uninfected controls [5,8,10]. Infection with C/R viruses and T/F viruses resulted in the significant depletion of tissue CD4 T cells. First, we compared CD4 T cell depletion in donor-matched cervical tissues infected with the T/F HIV-1 NL-1051.TD12.ecto to that infected with a control C/R HIV-1 variant NL-SF162.ecto. There was no statistical difference between the CD4 T cell depletion by these viruses (respectively 27.86628.6 and 57.07613.8 , n = 4, p = 0.67). Next, we pooled data 1676428 for all of the T/F and C/R HIV-1 variants used in the current study. These viruses respectively depleted 42.966.0 (median 35.26 , IQR [27.1 ?1.7 ], n = 19, p,0.0001) and 20.968.9 (median 27.32 IQR [3.01 ?5.65 ], n = 14, p = 0.025) of CD4 T cells. Thus, the depletion of CD4 T cells in tissues infected with these two types of HIV-1 variants was not different (p = 0.08) (Fig. 2). CD4 T cell depletion positively correlated with the proportion of infected cells in the remaining CD4 T cells as measured by flow cytometry (Spearman r = 0.5642, p,0.0001, n = 34). In tissues treated with 3TC, HIV-1 inoculation did not result in cell depletion: the fraction of CD4 T cells in such tissues was not statistically different from that in donor-matched uninfected tissues (n = 32, p.0.5).Finally, we compared activation status of CD4 T cells (Fig. 3) as evaluated by the expression of the following activation markers: CD25, CD38, CD69, CD95, and HLA-DR. In uninfected tissues these markers were respectively expressed by 11.2161.96 , 29.1164.3 , 77.3565.08 , 73.1268.81 , and 7.0761.29 of CD4 T cells (n = 24). As with the data regarding HIV-1 infection and CD4 T cell depletion we first compared activation of T cells by their expression of CD25, CD38, and HLA-DR in donor-matched tissues infected with a T/F HIV-1 construc.High background may obscure the actual viral production. Therefore, for further analysis, we evaluated HIV-1 tissue infection by enumerating CD4 T cells positive for intracellular p24 by flow cytometry. At 12 or 15 days post-infection, the tissues were digested and stained for intracellular p24. We detected p242expressing cells in tissues following exposure to all the tested HIV-1 variants (Fig. 1). To avoid the exclusion of CD4 T cells that may have down-regulated CD4 expression as a result of HIV-1 infection, we defined CD4 T cells as CD82CD3+ cells [9]. Initially, we inoculated tissue from three 22948146 donors in parallel with the T/F variant NL-1051.TD12.ecto and the C/R variant NLSF162.ecto. We found no statistical difference between the fractions of CD4 T cells infected by these viruses (respectively 14.1264 and 17.7465.9 , n = 3, p = 0.74). Neither were there statistically significant differences (p = 0.08) between the fractions of p242expressing CD4 T cells in the group of tissues infected with the C/R HIV-1 as compared to the group of tissues infected with T/F HIV-1. On average, the p24+ CD4 T cell fraction in C/ R HIV-1 infected tissues constituted 12.661.5 (median 12.6 , IQR [7.61 ?7.1 ] n = 19) of total CD4 T cells, while in tissues infected with T/F viruses this fraction constituted 8.2562.6 (median 3.76 , IQR [0.96 ?5.8 ], n = 14) (Fig. 1). Next, we estimated the depletion of CD4 T cells by comparing the ratio of CD8+ to CD4+ T cells (i.e. CD82CD3+) in infected and uninfected controls [5,8,10]. To pool data obtained from different donors, we normalized the data by expressing the CD4/ CD8 ratio in infected tissue as a percent of the same ratio in matched uninfected controls [5,8,10]. Infection with C/R viruses and T/F viruses resulted in the significant depletion of tissue CD4 T cells. First, we compared CD4 T cell depletion in donor-matched cervical tissues infected with the T/F HIV-1 NL-1051.TD12.ecto to that infected with a control C/R HIV-1 variant NL-SF162.ecto. There was no statistical difference between the CD4 T cell depletion by these viruses (respectively 27.86628.6 and 57.07613.8 , n = 4, p = 0.67). Next, we pooled data 1676428 for all of the T/F and C/R HIV-1 variants used in the current study. These viruses respectively depleted 42.966.0 (median 35.26 , IQR [27.1 ?1.7 ], n = 19, p,0.0001) and 20.968.9 (median 27.32 IQR [3.01 ?5.65 ], n = 14, p = 0.025) of CD4 T cells. Thus, the depletion of CD4 T cells in tissues infected with these two types of HIV-1 variants was not different (p = 0.08) (Fig. 2). CD4 T cell depletion positively correlated with the proportion of infected cells in the remaining CD4 T cells as measured by flow cytometry (Spearman r = 0.5642, p,0.0001, n = 34). In tissues treated with 3TC, HIV-1 inoculation did not result in cell depletion: the fraction of CD4 T cells in such tissues was not statistically different from that in donor-matched uninfected tissues (n = 32, p.0.5).Finally, we compared activation status of CD4 T cells (Fig. 3) as evaluated by the expression of the following activation markers: CD25, CD38, CD69, CD95, and HLA-DR. In uninfected tissues these markers were respectively expressed by 11.2161.96 , 29.1164.3 , 77.3565.08 , 73.1268.81 , and 7.0761.29 of CD4 T cells (n = 24). As with the data regarding HIV-1 infection and CD4 T cell depletion we first compared activation of T cells by their expression of CD25, CD38, and HLA-DR in donor-matched tissues infected with a T/F HIV-1 construc.