Reference Ranges for the Clinical Laboratory Derived from a Rural Population in Kericho, Kenya

The conduct of Phase I/II HIV vaccine trials internationally necessitates the development of region-specific clinical reference ranges for trial enrolment and participant monitoring. A population based cohort of adults in Kericho, Kenya, a potential vaccine trial site, allowed development of clinical laboratory reference ranges. Lymphocyte immunophenotyping was performed on 1293 HIV seronegative study participants. Hematology and clinical chemistry were performed on up to 1541 cohort enrollees. The ratio of males to females was 1.9∶1. Means, medians and 95% reference ranges were calculated and compared with those from other nations. The median CD4+ T cell count for the group was 810 cells/µl. There were significant gender differences for both red and white blood cell parameters. Kenyan subjects had lower median hemoglobin concentrations (9.5 g/dL; range 6.7–11.1) and neutrophil counts (1850 cells/µl; range 914–4715) compared to North Americans. Kenyan clinical chemistry reference ranges were comparable to those from the USA, with the exception of the upper limits for bilirubin and blood urea nitrogen, which were 2.3-fold higher and 1.5-fold lower, respectively. This study is the first to assess clinical reference ranges for a highland community in Kenya and highlights the need to define clinical laboratory ranges from the national community not only for clinical research but also care and treatment

Evaluation of the HIV-1 reverse transcriptase inhibitory properties of extracts from some medicinal plants in Kenya

Extracts from twenty two medicinal plants popularly used in preparing traditional remedies in Kenya were screened for activity against the HIV-1 reverse transcriptase. The screening procedure involved the use of tritium labeled thymidine triphosphate as the enzyme substrate and polyadenylic acid.oligodeoxythymidylic acid [poly(rA).p(dT)12-18] as the template primer dimer. Foscarnet was used as a positive control in these experiments. At a concentration of 100µg/ml, extracts from eight of these plants showed at least 50 per cent reverse transcriptase inhibition. This activity was abitrarily considered as significant. This indicates that there is the probability that some antiretroviral compounds could be identified and isolated from materials from these plants. [Afr. J. Health Sci. 2002; 9:81-90

Vaccine coverage of potential T-cell epitopes from the observed infections.

<p>Inserts from the candidate vaccines were analyzed for the proportion of nonamers that each of their respective immunogens covered within the infecting strains from the incident, higher-risk, and prevalent infection studies. For each immunogen, the epitope coverage comparisons were divided into the same pure and recombinant strain subsets used to generate Tables <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135124#pone.0135124.t001" target="_blank">1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135124#pone.0135124.t002" target="_blank">2</a>. The colored sections of each bar denote the proportion of coverage attributable to a perfect match (black) or mismatched (blue to gray) nonamer as indicted by the figure legend.</p

The Number and Complexity of Pure and Recombinant HIV-1 Strains Observed within Incident Infections during the HIV and Malaria Cohort Study Conducted in Kericho, Kenya, from 2003 to 2006

<div><p>Characterization of HIV-1 subtype diversity in regions where vaccine trials are conducted is critical for vaccine development and testing. This study describes the molecular epidemiology of HIV-1 within a tea-plantation community cohort in Kericho, Kenya. Sixty-three incident infections were ascertained in the HIV and Malaria Cohort Study conducted in Kericho from 2003 to 2006. HIV-1 strains from 58 of those individuals were full genome characterized and compared to two previous Kenyan studies describing 41 prevalent infections from a blood bank survey (1999–2000) and 21 infections from a higher-risk cohort containing a mix of incident and prevalent infections (2006). Among the 58 strains from the community cohort, 43.1% were pure subtypes (36.2% A1, 5.2% C, and 1.7% G) and 56.9% were inter-subtype recombinants (29.3% A1D, 8.6% A1CD, 6.9% A1A2D, 5.2% A1C, 3.4% A1A2CD, and 3.4% A2D). This diversity and the resulting genetic distance between the observed strains will need to be addressed when vaccine immunogens are chosen. In consideration of current vaccine development efforts, the strains from these three studies were compared to five candidate vaccines (each of which are viral vectored, carrying inserts corresponding to parts of <i>gag</i>, <i>pol</i>, and <i>envelope</i>), which have been developed for possible use in sub-Saharan Africa. The sequence comparison between the observed strains and the candidate vaccines indicates that in the presence of diverse recombinants, a bivalent vaccine is more likely to provide T-cell epitope coverage than monovalent vaccines even when the inserts of the bivalent vaccine are not subtype-matched to the local epidemic.</p></div

Pure subtype and recombinant virus distribution observed during the incident infection study.

<p>The proportion of pure subtype and recombinant strains for the Kericho, Kenya Tea Plantation (community cohort) incident infection study conducted from 2003 to 2006.</p

Vaccine coverage of potential T-cell epitopes from the observed infections.

<p>Inserts from the candidate vaccines were analyzed for the proportion of nonamers that each of their respective immunogens covered within the infecting strains from the incident, higher-risk, and prevalent infection studies. For each immunogen, the epitope coverage comparisons were divided into the same pure and recombinant strain subsets used to generate Tables <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135124#pone.0135124.t001" target="_blank">1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135124#pone.0135124.t002" target="_blank">2</a>. The colored sections of each bar denote the proportion of coverage attributable to a perfect match (black) or mismatched (blue to gray) nonamer as indicted by the figure legend.</p

Median distance between vaccine inserts and observed recombinant strains.

<p>^b Both Env inserts have significantly closer sequence similarity to the recombinants when compared to CMDR, TZC, or mosaic 2 (p < .01); however, KEA is not significantly closer to the recombinants than the mosaic 1 insert.</p><p>Median distance between vaccine inserts and observed recombinant strains.</p

Phylogenetic tree containing the recombinants from the incident, higher-risk, and prevalent HIV-1 infection studies.

<p>The phylogenetic relationships between incident recombinant strains from the community cohort (red), higher-risk cohort recombinant strains (blue), and prevalent infection recombinant strains (green) were constructed using the full-length genomes and appropriate pure subtype and recombinant reference sequences. Bootstrap values at relevant nodes are shown. The scale bar indicates a genetic distance of 10%.</p

Genome structures of 33 HIV-1 recombinant strains identified during this community cohort incident infection study.

<p>(a) The incident recombinant genomes are depicted in relation to the HXB2 reference strain. Each colored region represents the predicted parent subtype based on the results from Recombinant Breakpoint Analysis; subtype A1 is shown in red, A2 in pink, C in yellow, and D in blue. (b) The two A2D strains with similar structures are shown compared to the CRF16_A2D reference breakpoints from <a href="http://hiv.lanl.gov" target="_blank">hiv.lanl.gov</a>. The A2D strains do appear to be CRF16_A2D infections, but are not directly linked (see text).</p