A gp41-based heteroduplex mobility assay provides rapid and accurate assessment of intrasubtype epidemiological linkage in HIV type 1 heterosexual transmission Pairs

Development of Nested PCR-Heteroduplex Mobility Assay for Determination of Genetic Diversity in the Block 2 Region of the Plasmodium falciparum Merozoite Surface Protein 1 Gene

Genetic diversity of Plasmodium parasite has significantly related to malaria control and vaccine development. The P. falciparum merozoite surface protein 1 (Pfmsp1) gene is a commonly used molecular marker to differentiate genetic diversity. This study is aimed at developing a nested PCR-Heteroduplex Mobility Assay (nPCR-HMA) for determination of the block 2 of the Pfmsp1 gene. The MAD20 family allele of P. falciparum was used as a control for optimization of the annealing and polyacrylamide gel electrophoresis conditions. In order to evaluate the developed nPCR-HMA, 8 clinical P. falciparum isolates were examined for allelic variants. The results revealed 9 allelic variants. Our study indicated that the successful nPCR-HMA with good precision and accuracy offers a more rapid, efficient, and cheap method for large-scale molecular epidemiological studies as compared to nucleotide sequencing.

Couples' voluntary HIV counseling and testing provider training evaluation, Zambia

With the expansion of couples' voluntary HIV counseling and testing (CVCT) in urban Zambia, there is a growing need to evaluate CVCT provider trainings to ensure that couples are receiving quality counseling and care. We evaluated provider knowledge scores, pre- and post-training and predictors of pre- and post-training test scores. Providers operating in 67 government clinics in four Copperbelt Province cities were trained from 2008 to 2013 in three domains: counseling, rapid HIV laboratory testing and data management. Trainees received pre- and post-training tests on domain-specific topics. Pre- and post-training test scores were tabulated by provider demographics and training type, and paired t-tests evaluated differences in pre- and post-training test scores. Multivariable ANCOVA determined predictors of pre- and post-training test scores. We trained 1226 providers, and average test scores increased from 68.8% pre-training to 83.8% post-training (p < 0.001). Test scores increased significantly for every demographic group and training type (p < 0.001) with one exception-test scores did not significantly increase for those receiving counseling or data management training who had less than a high school education. In multivariable analysis, higher educational level and having a medical background were predictive of a higher pre-test score; higher pre-test scores and having a medical background were predictive of higher post-test scores. Pre- and post-test assessments are critical to ensure quality services, particularly as task-shifting from medical to lay staff becomes more common. Assessments showed that our CVCT trainings are successful at increasing knowledge, and that those with lower education may benefit from repeat trainings.

Inferring viral population structures using heteroduplex mobility and DNA sequence analyses

Heteroduplex mobility (HMA) and tracking assays (HTA) are used to assess genetic relationships between DNA molecules. While distinguishing relationships between clonal or nearly clonal molecules is relatively straightforward, inferring population structures is more complex. To address this issue, HIV-1 quasispecies with varying levels of diversity were studied using both HTA and DNA sequencing. Viral diversity estimates and the temporal features of virus evolution were found to be generally concordant between HTA and DNA sequencing. In addition, the distribution of pairwise differences and the rates of virus divergence were similar between the two methods. These findings support the use of HTA to characterize variant populations of DNA and strengthen previous inferences concerning the evolution of HIV-1 over the course of infection.

Use of the heteroduplex mobility assay and cell sorting to select genome sequences of the CCR5 gene in HEK 293T cells edited by transcription activator-like effector nucleases

Engineered nucleases such as zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN) are one of the most promising tools for modifying genomes. These site-specific enzymes cause double-strand breaks that allow gene disruption or gene insertion, thereby facilitating genetic manipulation. The major problem associated with this approach is the labor-intensive procedures required to screen and confirm the cellular modification by nucleases. In this work, we produced a TALEN that targets the human CCR5 gene and developed a heteroduplex mobility assay for HEK 293T cells to select positive colonies for sequencing. This approach provides a useful tool for the quick detection and easy assessment of nuclease activity.