Ce of the PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28878015 complete PTAP motif duplication in other subtypes, primarily in A and D for which PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27872238 a large number of sequences are available in the databases, is quite intriguing. Lastly, the length of the sequence duplication to constitute the additional NF-B motif appears to be fixed, 21 bases, and invariable in subtype C [5]. In contrast, the sequence length of PTAP duplication is highly variable in both subtypes B and C ranging from 4 to 16 amino acids [28, 35] (Fig. 5). Because of the complexity of viral quasispecies, we sequenced gag from the genomic DNA (data not shown) of the selected subjects and observed the PTAP duplication in the proviral compartment also. Analysis of sequences from the proviral compartment will not be the representative of the quasispecies circulating in the plasma, hence it was important to capture the presence of circulating virions using plasma viral RNA. It would be critical to know if the PTAP variant viral strains are likely to expand in the population in the coming years like the NF-B variant viral strains have been doing currently. At the population level, the relative success of an emerging variant viral strain primarily depends on the difference in the plasma viral loads of the two divergent variant strains, especially in a mixed Anlotinib chemical information infection where the single-PTAP and double-PTAP viral strains coexist in the same host. It is not known if PTAP duplication in Gag p6 modulates the infectivity properties of the envelope in any manner. Especially, in the context of a mixed infection, the PTAP divergent viral strains are not likely to differ from each other with respect to the envelope considering the enormous magnitude of viral recombination in vivo. The PTAP divergent viral strains sharing the same envelope, therefore, are expected to maintain identical biological properties, including cell tropism, the preferred route of transmission, and target cell populations. In a mixed infection, a viral variant such as the strain containing a double-PTAP motif represented by a profoundly higher magnitude of plasma viral load (unpublished data) is likely to be transmitted at a significantly higher rate to the new host. If this prediction holds true, the PTAP variant viral strains are expected to expand rapidly replacing the singlePTAP viral strains in the coming years. Furthermore, to address the question whether the PTAP motif duplication is associated with the expansion of the variant viral strains, we downloaded the available full-length Gag sequences of subtypes B and C from theLANL HIV sequence database. Using these sequences (3,647 and 1,787 representing subtypes B and C, respectively), we asked if the percentage prevalence of the viral strains containing the duplication increased over the past 30 years when stratified into 5-year phases starting from 1979 (Fig. 2b). Given the large sample size, the sequences are expected to be representative of the viral prevalence in the natural infection. In subtype B, the percent prevalence of the double-PTAP strains doubled between phases 1996?000 to 2001?005 from 3.4 to 6.5 and remained stable after that. A comparable trend was seen in the context of subtype C but at a higher prevalence. Between phases 1996?000 to 2001?005, the percent prevalence of the double-PTAP strains of subtype C increased from 17.6 to 25 and increased further to 31 prevalence in the final phase of 2010?015. Importantly, a progressively increasing prevalence of the double-PTAP viral strains was eviden.
