Performance of in-house assay versus prototype kit.

<p>The normalized MFI values (n) and avidity index (a) for the in-house assay and kit were compared for drug naïve, known recent (infected <6 months) and long-term (infected >1 year) specimens. The boxes represent the 25^th to 75^th percentile of reactivity, while the middle lines represent the median values. Black dots indicate the 5^th to 95^th percentile of reactivity. </p

Inter-laboratory kit performance.

<p>The normalized MFI values (n) and avidity index (a) of known recent and long-term specimens, as measured by the prototype kits, were compared for each laboratory. </p

Extensive Genetic Diversity of HIV-1 in Incident and Prevalent Infections among Malaysian Blood Donors: Multiple Introductions of HIV-1 Genotypes from Highly Prevalent Countries - Fig 3

<p><b>Sub-region neighbour joining tree analyses of the 1.6kb partial <i>gag-pol</i> genes sequenced in two clusters of (A) subtype B'/C and (B) B'/G recombinants characterised in the population.</b> Based on the informative sites analyses, recombination breakpoints were estimated for each strain and the partial <i>gag-pol</i> sequences (HXB2:1753–3440) were then sub-divided into different regions for phylogenetic reconstruction. Putative HIV-1 parental reference genotypes used in bootscan were 90THCM235 (CRF01_AE), CNRL42 (subtype B' of Thai origin), 95IN21068 (subtype C) and 01NGPL0674 (subtype G). Incident or prevalent HIV-1 infections for each strain, as determined using a limiting antigen avidity enzyme immunoassay (LAg-Avidity EIA) were identified by orange triangles or red circles, respectively. Bootstrap values of greater than 70% were indicated on the branch nodes. The scale bar represents 1% genetic distance (0.01 substitutions per site).</p

Phylogenetic reconstruction of 136 partial <i>gag-pol</i> gene sequences of 1.6kb amplified among the blood donors in Kuala Lumpur, Malaysia between 2013 and 2014.

<p>HIV-1 incidence was estimated using a limiting antigen avidity enzyme immunoassay (LAg-Avidity EIA) to identify recent (incident) and long-standing (prevalent) infections as indicated where available. Neighbour-joining tree was constructed in MEGA 5.05 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161853#pone.0161853.ref022" target="_blank">22</a>] using Kimura 2-parameter method of nucleotide substitutions and the reliability of the branching nodes were assessed by bootstrap analysis of 1000 replicates. Eleven partial <i>gag</i>-PR (834bp) and two RT gene sequences (966bp) were genotyped separately using similar methods and their prevalence was reported in this study (figures not shown for clarity). Relevant HIV-1 reference genotypes in Southeast Asia include subtype B, CRF01_AE, CRF33_01B, CRF34_01B, CRF48_01B, CRF52_01B, CRF53_01B, CRF54_01B, CRF58_01B and CRF74_01B. Reference sequences of other genotypes prevalent in China (CRF07_BC, CRF08_BC and other recently-described B'/C CRFs) and Africa (subtype G, CRF02_AG and CRF45_cpx) were also included in the analysis. The reference sequences were labelled in the following order: genotype, country of origin, isolate name and GenBank accession number. A well-supported cluster of Malaysian subtype G strains was also highlighted as G_MY within the subtype G clade of African reference strains. All 12 unique recombinant forms were denoted by closed diamonds and labelled according to incident or prevalent infection status. Clusters of novel B'/C recombinants (strains 13MYNBB108, 14MYNBB084, 14MYNBB090 and 14MYNBB164) and B'/G recombinants (13MYNBB064 and 13MYNBB065) were highlighted in the tree. Simian immunodeficiency virus (SIVcpz) reference strains were included as outgroup. Bootstrap values of greater than 70% were indicated on the branch nodes. The scale bar represents 1% genetic distance (0.01 substitutions per site).</p

HIV-1 genotype distribution of incident and prevalent infections among 127 blood donors in Kuala Lumpur.

<p>A limiting-antigen avidity enzyme immunoassay (LAg-Avidity EIA) was used to distinguish incident from prevalent HIV-1 infections. Out of 179 samples available for incidence assay testing, 70.9% (n = 127) were successfully genotyped and comprised of 29 (22.8%) incident HIV-1 infections.</p

Kaplan-Meier Survival Curves Showing the Probability of Remaining Free of P. falciparum Infection during the 11 wk of Surveillance

<p>Week 0 of surveillance began in October 2002, 14 d after the third dose of vaccine was administered.</p

Trial Profile

<p>Trial Profile</p

Identification of Acute (HIV Antibody Negative or Indeterminate) and Established (Confirmed HIV Antibody Positive) HIV Infections by Targeted Testing Programs in San Francisco, 2003–2008.

<p> = rapid test; IA = immunoassay. RT</p><p> Include results from the acute HIV screening program results for years 1998 through 2008.</p

Phylogenic tree of the HIV-1 sequences.

<p>Phylogenic tree of the HIV-1 sequences.</p

Characteristics of donors with drug resistance of potential low-level resistance or above (N = 27).

<p>Characteristics of donors with drug resistance of potential low-level resistance or above (N = 27).</p