We did not observe significant differences in the viral protease and integrase activities in viruses carrying the Pol products from B and C subtypes, but found that RT affected replication of the viruses in a subtype dependent man ner. selleck chemicals Specifically we showed that viruses carrying RT from subtype C isolates, as well as RT chimeras contain ing either the subtype C RT polymerase domain or con nection and RNase H domains, had decreased levels of viral cDNA accumulation, which correlated with reduced integration and lower levels of viral replication. The frequencies of nucleotide substitutions in the pro Inhibitors,Modulators,Libraries viral DNA were found to be similar. Results Characterization of Inhibitors,Modulators,Libraries subtype C HIV 1 pol genes The pol genes of three subtype C HIV 1 isolates were characterized.
The viruses were isolated from three peri natally Inhibitors,Modulators,Libraries infected, anti retroviral na ve Zambian infants. Isolates 1084i and 1984i were obtained from patients with slow disease Inhibitors,Modulators,Libraries progression, characterized by a pro longed clinically asymptomatic period, whereas isolate 2669i was associated with fast disease progression and a lethal outcome of the infected infant within the first year of life. We also selected two wild type subtype B strains, NL4 3 and YU 2 as comparisons. The Pol sequences of these viruses are similar to the subtype B consensus and have only 1. 29 and 1. 36% of AA differences from consensus sequence. The RT fragments within the Pol are relatively more variable and differ from sub type B consensus by 1. 6 and 2. 3% respectively. In contrast, the available subtype C variants are more heterogeneous.
The differences of RT AA sequences from subtype C consensus are ranging from 2. 4 to 2. 9%. Sequences of the RT polymerase domain from analyzed subtype C isolates Inhibitors,Modulators,Libraries 2669i, 1984i, and 1084i have from 3. 6 to 5. 6% diversity among them, whereas the difference between homologous sequences of NL4 3 and YU 2 isolates is 2. 6%. Comparison of the AA clusters in RT, which are distinct between selected isolates and consensus sequences of subtypes B and C indicates that the varying amino acids are not located in the motifs which are critical for the RT enzy matic activity. The presence of gag pol or pol fragments from HIV 1 subtype C correlates with decreased level of virus replication independently of viral backbone and the cell types It has been demonstrated that subtype C viruses do not replicate as well as subtype B and display lower replica tion fitness in primary CD4 T cells and peripheral blood mononuclears.
To determine whether the pol gene products have a subtype specific effect on the viral replication, we compared the replication things dynamics of a subtype B strain, NL4 3, and a chimeric NL4 3 based virus NL pol, which carried the 1084i pol gene without its protease domain, in Sup T1 cells. Virus replication was moni tored by measuring p24CA.