Mosaic structures of unique recombinant forms (URF) among men who have sex with men (MSM).

<p>The closely related putative parental strains for each URF were determined by similarity plot. The bootscan plots of <i>pro-rt</i> gene (HXB2∶2253–3275) with window size of 300 bp and step size of 30 bp illustrate the relationship of Malaysian URF to the reference strains of HIV-1 subtype B of western origin, CRF01_AE, subtype C and subtype A. The recombination breakpoint(s) in relation to HXB2 coordinates are indicated in the inset.</p

Basic demographic and baseline clinical characteristics of 103 HIV-1 patients initiating cART in Kuala Lumpur, Malaysia.

<p>Categorical variables are described as n (%) and numerical variables are described as mean (± SD) or median (IQR).</p><p>Abbreviations: HIV-1, human immunodeficiency type-1; cART, combination antiretroviral therapy; SD, standard deviation; IQR, interquartile range.</p><p>^ψ<i>P</i> values are given for test of general differences across the two subgroups using an independent t-test^€ for normally-distributed categorical outcomes and Mann-Whitney U test^Δ for non-normally-distributed continuous outcomes (<i>P</i> values of < .05 are considered significant).</p><p>^a data includes Malay, Indian and other minor ethnicities.</p><p>^b data includes men-who-have-sex-with-men (MSM), unsafe injecting drug use and blood transfusion.</p><p>^c the interval between the day of cART initiation and the last clinical consultation available.</p><p>^d includes co-infections with tuberculosis, hepatitis B or C virus (HBV/HCV).</p><p>Basic demographic and baseline clinical characteristics of 103 HIV-1 patients initiating cART in Kuala Lumpur, Malaysia.</p

Phylodynamic profile of HIV-1 subtype B and CRF01_AE among men who have sex with men (MSM) in Kuala Lumpur, Malaysia.

<p>The Malaysian MSM sequences (35 subtype B and 35 CRF01_AE) along with respective reference sequences were analyzed separately. For illustration purposes, all 70 MSM sequences were presented in the same maximum clade credibility (MCC) tree. (<b>A</b>) Bayesian’s MCC tree of 1022 bp <i>pro-rt</i> gene (HXB2∶2253–3275) of 70 Malaysian MSM sequence data collected between March 2006 and August 2012 and reference sequences (black branches) is shown. The Bayesian coalescent-based relaxed molecular clock model was performed in BEAST 1.7, with uncorrelated lognormal model nested in general time-reversible (GTR) nucleotide substitution model and a proportion of invariant sites. The Markov chain Monte Carlo (MCMC) analysis was computed for 50 million states sampled every 10,000 states and output was assessed for convergence by means of effective sampling size (ESS) after a 10% burn-in. Transmission clusters are defined based on strong statistical supports generated at the internal nodes of the maximum likelihood and MCC tree reconstructions (bootstrap values of more than 90% and posterior probability of 1, respectively). A total of 12 monophyletic transmission clusters of different sizes (2–7 sequences) were determined, of which 6 clusters (B.1– B.6) were found within the subtype B lineages (blue branches) and another 6 clusters (AE.1– AE.6) were identified within the CRF01_AE lineages (red branches). The mean tMRCA and 95% highest posterior distribution (HPD) for each cluster are indicated in parentheses. In addition, 25 single unique lineages (green branches) involving subtype B and CRF01_AE are indicated in the phylogenetic analysis. The scale bar indicates the time in years and the alphabet at the tip of each branch represents the ethnicity of the subject, namely Malay (M), Chinese (C), Indian (I) and others (O). (<b>B</b>) Bayesian skyline plots (BSPs) generated from 35 HIV-1 subtype B and 35 CRF01_AE heterochronously sampled <i>pro-rt</i> gene from the MSM population in Kuala Lumpur. The origin and changes in effective population size through time for subtype B and CRF01_AE in the country were estimated. The 95% HPD of the effective population size is indicated in dashed lines. (<b>C</b>) Relative posterior probability distribution of the tMRCAs for the respective subtype B and CRF01_AE transmission clusters.</p

Cox proportional hazards using unadjusted (univariate) and adjusted (multivariate) analyses to assess the effects of covariates on the rate of CD4+ T cell recovery, defined as time for CD4+ T-cell count increase to ≥350 cells/μL during cART.

<p>Abbreviations: cART, combination antiretroviral therapy; HR, hazard ratio; CI, confidence intervals; Ref, reference.</p><p>^a covariates with P values < .25 were included in the adjusted analysis. The rate of CD4+ T cell recovery was also adjusted for baseline HIV-1 RNA because it is known to be an important predictor of immunologic recovery.</p><p>Cox proportional hazards using unadjusted (univariate) and adjusted (multivariate) analyses to assess the effects of covariates on the rate of CD4+ T cell recovery, defined as time for CD4+ T-cell count increase to ≥350 cells/μL during cART.</p

Kaplan-Meier analysis of time to reach CD4+ T-cell count of ≥350 cells/μL (<i>A</i>) or to ≥500 cells/μL (<i>B</i>) in patients infected with CRF01_AE and subtype B on cART.

<p><i>P</i> values were calculated using log-rank test.</p

The bootscanning plots of 26 near-full-length sequences and 6 half-genome sequences of HIV-1 strains isolated from Dehong IDUs with diagnosis year in chronological order.

<p>In the recombination analyses, a subtype C strain from India (95IN21068) (pink) and a subtype B′ strain from Yunnan (RL42) (blue) was used as subtype references, and a CRF01_AE strain from Thailand (CM240) (green) was used as an out-group control.</p

A formylpeptide receptor, FPRL1, acts as an efficient coreceptor for primary isolates of human immunodeficiency virus-2

viral inoculation. The coreceptor uses of these HIV-1 strains are summarized (see Additional file ). NP-2/CD4 cells were also tested up to eight days after inoculation and were completely resistant to all the HIV-1 strains examined.<p><b>Copyright information:</b></p><p>Taken from "A formylpeptide receptor, FPRL1, acts as an efficient coreceptor for primary isolates of human immunodeficiency virus"</p><p>http://www.retrovirology.com/content/5/1/52</p><p>Retrovirology 2008;5():52-52.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2453146.</p><p></p

Additional file 3: Figure S3. of Molecular epidemiology and evolutionary histories of human coronavirus OC43 and HKU1 among patients with upper respiratory tract infections in Kuala Lumpur, Malaysia

Phylogenetic analysis of the HCoV-OC43 1a gene (nsp3). Tree was reconstructed using neighbor-joining method. Bootstrap values were calculated from 1,000 trees. Bootstrap values of greater than 70% were indicated on the branch nodes. The scale bar of individual tree was indicated in substitutions per site, using Kimura 2-parameter model in MEGA (version 5.1) to estimate pair-wise evolutionary distance. The Malaysian isolates obtained in this study were color-coded. Each HCoV-OC43 sequence was assigned to its proper genotype based on the S1 phylogenetic analysis. (PDF 284 kb

Maximum clade credibility (MCC) trees reconstruction of CRF51_01B isolated in Singapore and Malaysia.

<p>MCC trees for protease (subtype B, HXB2∶2253–2627, 375 bp), gp120 (CRF01_AE, HXB2∶6942–7571, 630 bp) and gp41 regions (subtype B, HXB2∶7803–8276, 474 bp) are shown. Timescale is shown at the bottom of the tree. The mean tMRCA and 95% highest probability density (HPD) for the key nodes are indicated. CRF51_01B strains from Malaysia are highlighted in orange.</p

HIV-1 genotype characterizations of Dehong IDU subjects.

*<p>These sequences were not included in the subtype related factors analysis.</p>†<p>5′ half genome sequences.</p>‡<p>3′ half genome sequences.</p>§<p>Genotype was determined based on all sequences available.</p