A tightly clustered hepatitis E virus genotype 1a is associated with endemic and outbreak infections in Bangladesh.

BACKGROUND: Hepatitis E virus (HEV) infection is endemic in Bangladesh and there are occasional outbreaks. The molecular characteristics and pathogenesis of endemic and outbreak HEV strains are poorly understood. We compared the genetic relatedness and virulence associated mutations of endemic HEV strains with outbreak strains. METHODS: We analyzed systematically collected serum samples from HEV immunoglobulin M (IgM) positive patients attended at Bangabandhu Sheikh Mujib Medical University, Dhaka from August 2013 to June 2015. HEV RNA positive samples were subjected to whole genome sequencing. Genotype and subtype of the strains were determined by phylogenetic analysis. Virulence associated mutations e.g. acute viral hepatitis (AVH), fulminant hepatic failure (FHF), chronic hepatitis, ribavirin treatment failure (RTF), B and T cell neutralization epitopes were determined. RESULTS: 92 HEV immunoglobulin M (IgM) antibody positive plasma samples (43 in 2013-2014 and 49 in 2014-2015) were studied. 77.1% (70/92) of the samples were HEV RNA positive. A 279 bp open reading frame (ORF) 2 and ORF 3 sequence was obtained from 54.2% (38/70) of the strains. Of these 38 strains, whole genome sequence (WGS) was obtained from 21 strains. In phylogenetic analysis of 38 (279 bp) sequence all HEV sequences belonged to genotype 1 and subtype 1a. Further phylogenetic analysis of 21 HEV WGS, Bangladeshi HEV sequences clustered with genotype 1a sequences from neighboring countries. Within genotype 1a cluster, Bangladesh HEV strains formed a separate cluster with the 2010 HEV outbreak strains from northern Bangladesh. 80.9 to 100% of the strains had A317T, T735I, L1120I, L1110F, P259S, V1479I, G1634K mutations associates AVH, FHF and RTF. Mutations in T cell recognition epitope T3, T5, T7 was observed in 76.1%, 100% and 100% of the strains respectively. CONCLUSION: Strains of HEV genotype 1a are dominant in Bangladesh and are associated with endemic and outbreak of HEV infection. HEV isolates in Bangladesh have high prevalence of virulence associated mutations and mutation which alters antigenicity to B and T cell epitopes

Experience in establishing a high-risk biocontainment facility in response to COVID-19 pandemic under resource constrain settings

The health care systems in resource limited countries are facing major challenges in dealing with Coronavirus disease (COVID-19). In Bangladesh, a steady increase in the number of COVID-19 cases since its first report on March 8, 2020, has led to an increased demand for COVID-19 detection facilities throughout the country. The detection of severe acute respiratory syndrome (SARS-CoV-2), the causative organism of COVID-19 and a highly infectious group 3(three) organism, requires a high biocontainment laboratory with a certain standard prerequisite infrastructure. This study describes the necessary steps for establishing and running a COVID-19 laboratory under resource constraint settings. Our experience indicates that, with collaborative efforts, funding, and technical support from locally available expertise, it is feasible to set up an optimally functional biocontainment facility with an acceptable quality performance despite several short comings. BSMMU J 2021; 14 (COVID -19 Supplement): 45-5

Nuclear magnetic resonance based profiling of biofluids reveals metabolic dysregulation in HIV-infected persons and those on anti-retroviral therapy.

BACKGROUND: Although HIV causes immune deficiency by infection and depletion of immunocytes, metabolic alterations with clinical manifestations are also reported in HIV/AIDS patients. Here we aimed to profile metabolite changes in the plasma, urine, and saliva of HIV/AIDS patients, including those on anti-retroviral therapy (ART). METHODS: Metabolic profiling of biofluids collected from treatment naïve HIV/AIDS patients and those receiving ART was done with solution-state nuclear magnetic resonance (NMR) spectroscopy followed by statistical analysis and annotation. RESULTS: In Principal Component Analysis (PCA) of the NMR spectra, Principal Component 1 (PC1) alone accounted for 99.3%, 87.2% and 78.8% variations in plasma, urine, and saliva, respectively. Partial least squares discriminant analysis (PLS-DA) was applied to generate three-component models, which showed plasma and urine to be better than saliva in discriminating between patients and healthy controls, and between ART-naïve patients and those receiving therapy. Twenty-six metabolites were differentially altered in any or two types of samples. Our results suggest that urinary Neopterin, and plasma Choline and Sarcosine could be used as metabolic biomarkers of HIV/AIDS infection. Pathway analysis revealed significant alternations in 12 metabolic pathways. CONCLUSIONS: This study catalogs differentially regulated metabolites in biofluids, which helped classify subjects as healthy controls, HIV/AIDS patients, and those on ART. It also underscores the importance of further studying the consequences of HIV infection on host metabolism and its implications for pathogenesis

MicroRNA-150 is a potential biomarker of HIV/AIDS disease progression and therapy.

BACKGROUND: The surrogate markers of HIV/AIDS progression include CD4 T cell count and plasma viral load. But, their reliability has been questioned in patients on anti-retroviral therapy (ART). Five microRNAs (miRNAs) - miR-16, miR-146b-5p, miR-150, miR-191 and miR-223 in peripheral blood mononuclear cells (PBMCs) were earlier found to assign HIV/AIDS patients into groups with varying CD4 T cell counts and viral loads. In this pilot study, we profiled the expression of these five miRNAs in PBMCs, and two of these miRNAs (miR-146b-5p and miR-150) in the plasma of HIV/AIDS patients, including those on ART and those who developed ART resistance, to evaluate if these are biomarkers of disease progression and therapy. RESULTS: We quantified miRNA levels by quantitative reverse transcription polymerase chain reaction (qRT-PCR) using RNA isolated from PBMCs and plasma of healthy persons or HIV-infected patients who were (1) asymptomatic; (2) symptomatic and ART naïve; (3) on ART; and (4) failing ART. Our results show miR-150 (p<0.01) and to a lesser extent miR-146b-5p (p<0.05) levels in PBMCs to reliably distinguish between ART-naïve AIDS patients, those on ART, and those developing drug resistance and failing ART. The plasma levels of these two miRNAs also varied significantly between patients in these groups and between patients and healthy controls (p values <0.05). CONCLUSIONS: We report for the first time that PBMC and plasma levels of miR-150 and miR-146b-5p are predictive of HIV/AIDS disease progression and therapy

Assessment of HIV disease progression before and after initiation of anti­retroviral therapy by CD4 & CD8 T-lymphocyte count and viral load assay

Backgrounds: As there is no published data regarding the response to Anti-retroviral therapy (ART) among HIV patients from Bangladesh. The present study was designed to determine the immunological and virological responses of HIV infected Bangladeshi adults starting ART. Objectives: To monitor the changes of CD4 and CD8 T-lymphocyte count and Viral load (VL) before and after three and six months of starting ART. Methods: 20 symptomatic HIV infected patients with CD4 T-lymphocyte count of <350 cells/µ] of blood were initiated ART.CD4 and CDS T-lymphocyte counts were estimated by Flowcytometer and VL was dete1mined by real-time PCR technique. Results: The mean CD4 T-lymphocyte count among the sn1dy patients were 177±127 cells/µl before initiation of ART. After ART initiation, their mean CD4 count increased significantly to 368±181 and 452±183 cellshll after three and six months respectively (P0.05). Before ART initiation, the mean VL was 5.25±1.19 log10 (copies/ml) among the study population which became undetectable in 15 (75%) patients after three months of ART and in another 2 (10%) patients after 6 months of ART initiation. Conclusion: Our study concluded that, ART is effective in slowing the progression of HIV infection to AIDS with good immunological and virological outcome among the ART initiators

Assessment of HIV disease progression before and after initiation of anti­retroviral therapy by CD4 & CD8 T-lymphocyte count and viral load assay

Backgrounds: As there is no published data regarding the response to Anti-retroviral therapy (ART) among HIV patients from Bangladesh. The present study was designed to determine the immunological and virological responses of HIV infected Bangladeshi adults starting ART. Objectives: To monitor the changes of CD4 and CD8 T-lymphocyte count and Viral load (VL) before and after three and six months of starting ART.Methods: 20 symptomatic HIV infected patients with CD4 T-lymphocyte count of &lt;350 cells/µ] of blood were initiated ART.CD4 and CDS T-lymphocyte counts were estimated by Flowcytometer and VL was dete1mined by real-time PCR technique.Results: The mean CD4 T-lymphocyte count among the sn1dy patients were 177±127 cells/µl before initiation of ART. After ART initiation, their mean CD4 count increased significantly to 368±181 and 452±183 cellshll after three and six months respectively (P&lt;0.0001).The mean CDS T-lymphocyte counts were 901±650 cells/µ! before initiation of ART, which increased to I 085±393 and 1121±372 cells/µl after three and six months respectively after ART initiation (P&gt;0.05). Before ART initiation, the mean VL was 5.25±1.19 log10 (copies/ml) among the study population which became undetectable in 15 (75%) patients after three months of ART and in another 2 (10%) patients after 6 months of ART initiation.Conclusion: Our study concluded that, ART is effective in slowing the progression of HIV infection to AIDS with good immunological and virological outcome among the ART initiators

Metabolic pathways modulated in HIV/AIDS patients.

<p>The pathways that have at least 2 metabolites in the “hits” list and are differentially regulated in HIV/AIDS are shown.</p

Details of clinical samples.

<p>Details of clinical samples.</p

Box and whisker plots showing the levels of representative metabolites in plasma, urine, and saliva collected from healthy controls (red), HIV/AIDS patients (green), and patients on ART (blue).

<p>The y-axis shows the normalized concentrations of the metabolites.</p

Parital least squares discrimination assay (PLS-DA) two-dimensional score plots developed from the ¹H NMR spectra of plasma, urine, and saliva collected from healthy control (X) and HIV/AIDS patients (Δ), and HIV/AIDS patients on ART (+).

<p>Parital least squares discrimination assay (PLS-DA) two-dimensional score plots developed from the ¹H NMR spectra of plasma, urine, and saliva collected from healthy control (X) and HIV/AIDS patients (Δ), and HIV/AIDS patients on ART (+).</p