Phylogenetic analysis of HIV <i>gag</i> gene (p24-p7) sequences (nt 1577–2040, HXB2) from HIV infected Nairobi residents.

<p>This tree (neighbor-joining) was created by aligning the selected sequences with reference sequences from Los Alamos database shown in bold). The sequence F1.FR.96.MP411 was selected as the out group.</p

Neighbor-Joining Phylogenetic trees of the three most represented subtypes, A (Fig. 2A), D (Fig. 2B) and C (Fig. 2C), depicting geographical associations of the studied sample group with other global regions.

<p>Reference Sequences from Los Alamaos Database have been indicated in bold. Out groups selected for Fig. 2A, B, and C were, respectively, A.EE.02.EST2002 394, NL.x.M12020, and IL.98.98IS002.</p

Distribution of HIV-1 subtypes in the studied population.

<p>Distribution of HIV-1 subtypes in the studied population.</p

Distribution of study subjects on the basis of gender, age, occupation, ethnicity and risk factors.

<p>Distribution of study subjects on the basis of gender, age, occupation, ethnicity and risk factors.</p

Complete blood count standard deviation ratios for age and sex.

<p>Complete blood count standard deviation ratios for age and sex.</p

Parametric complete blood count reference intervals after latent abnormal value exclusion.

<p>Parametric complete blood count reference intervals after latent abnormal value exclusion.</p

Flow diagram for recruitment.

<p>BMI: body mass index, CBC: complete blood count, DM: diabetes mellitus, HIV: Human Immunodeficiency Virus, HTN: hypertension *On antibiotics, blood donation in past 3 months, on treatment for hypothyroidism, > 65 years, > 65 years and hypertensive, rheumatic heart disease, prostate cancer.</p

Sex and age-related changes for representative parameters.

<p>F: female, Ferr: ferritin, Hb: haemoglobin, M: male, MCV: mean corpuscular volume, Plt: platelet count, RBC: red blood cell count, SDR: standard deviation ratio, Tf: transferrin.</p

Descriptive characteristics of participants (Median, 2.5~97.5 percentile).

<p>Descriptive characteristics of participants (Median, 2.5~97.5 percentile).</p

Graphical comparison of reference intervals (RIs) for WBC related parameters and platelets.

<p>Three bars for each study represent RIs for male+female (MF) in grey, male (M) in blue, and female (F) in red. RIs of this study is shown on top of each panel. The background shades in blue and pink represent RIs of this study for males and females. WBC: white blood cell count, Neu: Neutrophil, Lym: lymphocyte, Mon: monocyte, Eos: eosinophil, abs-absolute count, Plt-platelet count ¹<b>Exclusion criteria</b>: BMI > 35 kg/m², consumption of ethanol ≥ 70 g per day, smoking more than 20 tobacco cigarettes per day, chronic illness, recent recovery from acute illness, injury or surgery requiring hospitalization, known carrier state of HBV, HCV or HIV, pregnant or within 1 year after child birth. <b>CBC analyser</b>: Beckman Coulter ACT 5 DIFF CP analyser (Brea, California, US). ²<b>Exclusion criteria</b>: Febrile, pregnant, HIV seropositive, screen positive for syphilis and malaria. <b>CBC analyser</b>: ACT 5Diff CP instrument (Beckman Coulter, Fullerton, CA, USA) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198444#pone.0198444.ref007" target="_blank">7</a>]. ³<b>Exclusion criteri</b>a: HIV positive, pregnant. <b>CBC analyser</b>: Coulter ACT 5Diff CP analyser (Beckman Coulter, France) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198444#pone.0198444.ref018" target="_blank">18</a>]. ⁴<b>Exclusion criteria</b>: HIV positive, moribund, mentally ill, institutionalized persons, missing personal or laboratory data. <b>CBC analyser</b>: Act 5 Diff instrument (Beckman Coulter) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198444#pone.0198444.ref019" target="_blank">19</a>]. ⁵<b>Exclusion criteria</b>: Acutely ill, significant findings on physical examination or if laboratory tests revealed that they were pregnant, HIV antibody positive, had evidence of hepatitis B or C infection or suspected syphilis. <b>CBC analyser</b>: Beckman Coulter AcT 5 diff CP (Beckman Coulter, USA) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198444#pone.0198444.ref006" target="_blank">6</a>]. ⁶<b>Exclusion criteria</b>: HIV positive, presence of any illness as defined by the World Health Organization staging systems for HIV infection and disease. <b>CBC analyser</b>: Coulter counter T540 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198444#pone.0198444.ref020" target="_blank">20</a>]. ⁷<b>Exclusion criteria</b>: HIV positive, pregnant or on medication, body temperature ≥37.5°C or if clinical assessment revealed other signs or symptoms of disease that could influence the laboratory parameters of interest. <b>CBC analyser</b>: Sysmex KX-21N analyser (Sysmex Corp., Kobe, Japan) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198444#pone.0198444.ref021" target="_blank">21</a>]. ⁸<b>Exclusion criteria</b>: Alcohol abuse, medication, smoking, pregnant, breastfeeding, on oral contraception, on menses. <b>CBC analyser</b>: Coulter AcT 5diff and Sysmex KX-21N (Sysmex Corporation, Kobe, Japan) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198444#pone.0198444.ref022" target="_blank">22</a>]. ⁹<b>Exclusion criteria</b>: Acute or chronic respiratory, cardiovascular, gastrointestinal, hepatic or genitourinary conditions, blood donation or transfusion within the past 3 months, hospitalisation within past 1 month, any findings that would compromise laboratory parameters, pregnant or lactating mothers. <b>CBC analyser</b>: Micros 60 analysers (Horiba-ABX, Montpellier, France) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198444#pone.0198444.ref023" target="_blank">23</a>]. ¹⁰<b>Exclusion criteria</b>: HIV, HBV, and HCV viral infection, malaria, abnormal haemoglobin electrophoresis screening, presence of hypochromia. <b>CBC analyser</b>: Sysmex SF-3000 (Sysmex, Kobe, Japan) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198444#pone.0198444.ref024" target="_blank">24</a>]. ¹¹<b>Exclusion criteria</b>: HIV, current clinical symptoms, immunosuppressive or corticosteroid medication, chemotherapy, hospitalizations, surgery or blood transfusions in the six months prior to screening, splenomegaly, pregnant, Hb < 12 g/dL. Menstruating women returned in 2 weeks. <b>CBC analyser</b>: Beckman Coulter LH 750 (Beckman Coulter, Fullerton, CA, USA) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198444#pone.0198444.ref025" target="_blank">25</a>].</p