Understanding of cervical cancer, acceptability of HPV self-collection, and prevalence of HPV in a semi-urban setting in Bangladesh.

Human Papillomavirus (HPV) self-sampling has been implemented successfully as an alternative to traditional forms of cervical cancer screening in low-resource settings. Through Bangladesh's current national cervical cancer screening program, only about 10% of the at-risk population is reached. Thus, Bangladesh is an ideal setting to consider HPV self-sampling to improve cervical cancer prevention efforts. However, the feasibility and acceptability of HPV self-sampling has not been evaluated in Bangladesh. We aimed to understand levels of HPV and cervical cancer knowledge and to evaluate the feasibility and acceptability of HPV self-sampling for cervical cancer screening in a semi-urban Bangladeshi community. Participants were recruited from a local clinic; 164 women completed a cross-sectional questionnaire about attitudes towards screening, and cervical cancer and HPV risk factor knowledge, and provided self-collected cervical samples for high-risk HPV testing. Of the participants, 4.3% tested positive for high-risk HPV and were referred for appropriate follow-up care. Nearly all participants had heard of cervical cancer, though specific knowledge was quite low. Self-sampling for high-risk HPV testing had high rates of acceptability, high rates of convenience, and very little discomfort and embarrassment reported in this study population, making implementing HPV self-sampling as a form of cervical cancer screening in Bangladesh appear feasible.

Investigating the Association Between ABO Blood Groups and Rhesus Factors with Dengue and Chikungunya Virus Infections During the 2017 Outbreak in Bangladesh.

This retrospective study was conducted in 2017 during the dual dengue and chikungunya outbreak in Bangladesh. Febrile participants underwent blood tests for chikungunya, dengue, and ABO groups and rhesus (Rh) factors. Blood grouping information was gathered from healthy donors. Males and those aged between 18 and 49 years had a higher risk of contracting dengue and chikungunya. Blood group O exhibited the highest infection rates at ∼50%, whereas group AB had the lowest at ∼9% among the participants in the study. Yet, when considering the general population's blood group distribution, the combined odds of infection were 2.0, 3.5, and 1.4 times higher in groups B, O, and AB, respectively, than in group A. Infection rates were greater in Rh-negative people. Blood groups B, O, and AB showed higher susceptibility than blood group A according to adjusted odds ratios. Blood groups ABO and Rh factor hold significance in disease susceptibility and vaccine effectiveness. Keeping these implications in mind, further investigations are necessary to understand the mechanisms underlying these connections and their effects on the efficacy of dengue and chikungunya vaccines.

Intrinsic Apoptotic Pathway Genes of Circulating Blood Neutrophils Triggered during HIV Infection and Remained Stimulated in ART Patients.

BACKGROUND: The intrinsic apoptotic pathway of neutrophils in Human Immunodeficiency Virus (HIV) infection results in spontaneous neutrophil death. There is a scarcity of data regarding the gene expression of an intrinsic apoptotic pathway of neutrophils in HIV patients. OBJECTIVE: The objective of this study was to observe the differential expression of some important genes involved in the intrinsic apoptotic pathway of HIV patients, including those who were receiving antiretroviral therapy (ART). METHODS: Blood samples were collected from asymptomatic, symptomatic, ART receiver HIV patients, and healthy individuals. Total RNA was extracted from neutrophils and subjected to quantitative real-time PCR assay. CD4+T cells and an automated complete blood count were performed. RESULTS: Among the asymptomatic, symptomatic, and ART receiver HIV patients (n=20 in each group), median CD4+T counts were 633, 98, and 565 cells/ml, and the length of HIV infection in months (± SD) was 24.06 ± 21.36, 62.05 ± 25.51, and 69.2 ± 39.67, respectively. Compared with healthy controls, intrinsic apoptotic pathway genes, i.e., BAX, BIM, Caspase-3, Caspase-9, MCL-1, and Calpain-1, were upregulated to 1.21 ± 0.33, 1.8 ± 0.25, 1.24 ± 0.46, 1.54 ± 0.21, 1.88 ± 0.30, and 5.85 ± 1.34 fold in the asymptomatic group, and even more significantly, i.e., 1.51 ± 0.43, 2.09 ± 1.13, 1.85 ± 1.22, 1.72 ± 0.85, 2.26 ± 1.34, and 7.88 ± 3.31 fold in symptomatic patients, respectively. Despite CD4+ T-cell levels increased in the ART receiver group, these genes did not approach the level of healthy or asymptomatic and remained significantly upregulated. CONCLUSION: The genes involved in the intrinsic apoptotic pathway in circulating neutrophils during HIV infection were stimulated in vivo, and ART reduced the expression of those upregulated genes but did not return to the level of asymptomatic or healthy individuals.

Use of whole blood and dried blood spot for detection of HIV-1 nucleic acids using reverse transcription loop-mediated isothermal amplification.

For monitoring viral load (VL) or Early Infant Diagnosis (EID) of HIV-1, real-time Polymerase Chain Reaction (qPCR) is used to perform on plasma or Dried Blood Spot (DBS) sample. The qPCR method is expensive and requires sophisticated equipment. Therefore, there is a requirement for newer and cheaper technology for VL measurement or EID. In this analytical study, a Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) assay was optimized and applied for amplification of HIV nucleic acids (NA) extracted from plasma, heat-treated plasma, heat-treated whole blood and lysis buffer-treated dried blood spot (DBS). The amplified product of RT-LAMP assay was detected by color change of Hydroxy naphthol blue (HNB) dye, step ladder pattern band on agarose gel after electrophoresis and sigmoid-shaped curve in the real-time thermal cycler. Comparing the results from RT-LAMP testing of all conditions with the results obtained by RT-qPCR results, viewed as the gold standard; a relative analytical sensitivity and specificity of RT-LAMP was calculated as 100 % and 90 % respectively. The corresponding positive predictive value (PPV) and negative predictive value (NPV) were 93.75 % and 100 %, respectively. The percentage of agreement between the RT-LAMP and RT-qPCR was 88.46% and Cohen's kappa value was 0.75 shows a substantial agreement between the two tests. This study suggests that whole blood or DBS may be useful specimens for analysis by HIV-1 specific RT-LAMP, to provide a cost effective alternative to RT-qPCR for the detection of HIV-1 nucleic acid at the point of care, or in early infant diagnoses.

Genome Sequencing of Omicron Variants of SARS-CoV-2 Circulating in Bangladesh during the Third Wave of the COVID-19 Pandemic.

The coding-complete genome sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was obtained from 39 nasopharyngeal swab samples collected in January 2022 from Dhaka, Bangladesh, during the 3rd wave of the COVID-19 pandemic, using Illumina MiniSeq sequencing technology. Sequence analysis showed that all of them belonged to the WHO-designated variant of concern (VOC) Omicron. The presence of different sublineages of Omicron was noted, among which sublineage BA.2 (Nextstrain clade 21L) was the most prevalent one.

Genomic Surveillance of SARS-CoV-2 Viruses Collected during the Ending Phase of the First Wave of the COVID-19 Pandemic in Bangladesh.

Mutations, deletions, and the emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may pose a serious health threat. Here, we report the genome sequences of SARS-CoV-2 viruses that were collected from SARS-CoV-2-infected patients during the end phase of the first wave of the COVID-19 pandemic in Dhaka, Bangladesh.

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.

Persistence of SARS-CoV-2 RNA in a male with metabolic syndrome for 72 days: A case report.

Coronavirus disease-19 (COVID-19) was first identified in Wuhan, China, and spread gradually throughout the world. There are multiple reports of prolonged viral shedding in people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, such findings have not been documented in Bangladesh. Herein, we present a case of metabolic syndrome that remained positive for SARS-CoV-2 RNA over a prolonged period. On clinical and laboratory examination, the patient was diagnosed with obesity, raised blood pressure, dyslipidemia, and uncontrolled glycemia. However, upon taking appropriate measures and controlling the plasma sugar level, he tested negative for SARS-CoV-2 RNA on the 72nd day since illness onset. We observed that COVID-19 patients with several comorbidities, such as metabolic syndrome, may shed the virus over a prolonged period. Therefore, strict public health measures and isolation rules should be followed by a high-risk population.

Acceptance of a Symptom-Based Approach for COVID-19 rtRT-PCR Testing to Conserve Resources in a Lower Middle-Income Setting.

SARS-CoV-2 initially emerged in Wuhan, China in late 2019. It has since been recognized as a pandemic and has led to great social and economic disruption globally. The Reverse Transcriptase Real-Time Polymerase Chain Reaction (rtRT-PCR) has become the primary method for COVID-19 testing worldwide. The method requires a specialized laboratory set up. Long-term persistence of SARS-CoV-2 RNA in nasopharyngeal secretion after full clinical recovery of the patient is regularly observed nowadays. This forces the patients to spend a longer period in isolation and test repeatedly to obtain evidence of viral clearance. Repeated COVID-19 testing in asymptomatic or mildly symptomatic cases often leads to extra workload for laboratories that are already struggling with a high specimen turnover. Here, we present 5 purposively selected cases with different patterns of clinical presentations in which nasopharyngeal shedding of SARS-CoV-2 RNA was observed in patients for a long time. From these case studies, we emphasized the adoption of a symptom-based approach for discontinuing transmission-based precautions over a test-based strategy to reduce the time spent by asymptomatic and mildly symptomatic COVID-19 patients in isolation. A symptom-based approach will also help reduce laboratory burden for COVID-19 testing as well as conserve valuable resources and supplies utilized for rtRT-PCR testing in an emerging lower-middle-income setting. Most importantly, it will also make room for critically ill COVID-19 patients to visit or avail COVID-19 testing at their convenience.

Challenges in the establishment of a biosafety testing laboratory for COVID-19 in Bangladesh.

At the beginning of the coronavirus disease 2019 (COVID-19) pandemic in Bangladesh, there was a scarcity of ideal biocontainment facilities to detect the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a risk group of 3 organisms. Molecular detection of SARS-CoV-2 must be performed in a BSL-2 laboratory with BSL-3-equivalent infection prevention and control practices. Establishing these facilities within a short timeframe proved to be an enormous challenge, including locating a remote space distant from the university campus to establish a laboratory, motivating the laboratory staff to work with a novel pathogen without any prior experience, allocation of funds for essential equipment and accessories, and arrangement of a safe waste management system for environmental hazard reduction. This report also highlights several limitations, such as the facility's architectural design that did not follow the biosafety guidelines, lack of continuous flow of funds, and an inadequate number of laboratory personnel. This article describes various efforts taken to overcome the challenges during the establishment of this facility that may be adopted to create similar facilities in other regions of the country. Establishing a BSL-2 laboratory with BSL-3-equivalent infection prevention and control practices will aid in the early detection of a large number of cases, thereby isolating persons with COVID-19, limiting the transmission of SARS-CoV-2, and promoting a robust public health response to contain the pandemic.

Detection of SARS-CoV-2 RNA in conjunctival swab of a COVID-19 patient: The first report from Bangladesh.

Coronavirus disease-19 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 RNA (SARS-CoV-2 RNA). It usually manifests by fever and/or respiratory illness. Here, we present a case of COVID-19 patient who initially presented ocular symptoms like redness, itching, and watery discharge. Afterward, the patient developed fever and anosmia suggestive of COVID-19 disease. Nasopharyngeal swab and conjunctival swab test for SARS-CoV-2 RNA revealed positive by reverse-transcriptase real-time polymerase chain reaction. The patient was managed symptomatically at home and did not require any hospital admission. On day 12, the patient clinically recovered fully and his follow-up testing for SARS-CoV-2 RNA of both conjunctival swab and nasopharyngeal swab became undetected. This report emphasized that conjunctival mucosa may be considered as a portal of entrance for SARS-CoV-2 RNA in addition to the respiratory route. This study highlighted that any kind of ocular manifestations, such as conjunctival hyperemia, chemosis, watery discharge, periorbital erythema, and burning sensation should never be overlooked for probable COVID-19 in current pandemic settings. Moreover, strict eye protection using goggles/face shield should be used by all health care workers despite any working environment while caring for patients with or without COVID-19-related signs.

Molecular characterization of hepatitis B virus in Bangladesh reveals a highly recombinant population.

The natural history and treatment outcome of hepatitis B viruses (HBV) infection is largely dependent on genotype, subgenotype, and the presence or absence of virulence associated mutations. We have studied the prevalence of genotype and subgenotype as well as virulence and drug resistance associated mutations and prevalence of recombinant among HBV from Bangladesh. A prospective cross-sectional study was conducted among treatment naïve chronic HBV patients attending at Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh for HBV viral load assessment between June and August 2015. Systematical selected 50% of HBV DNA positive patients (every second patient) were enrolled. Biochemical and serological markers for HBV infection and whole genome sequencing (WGS) was performed on virus positive sample. Genotype, subgenotype, virulence, nucleos(t)ide analogue (NA) resistance (NAr) mutations, and the prevalence of recombinant isolates were determined. Among 114 HBV DNA positive patients, 57 were enrolled in the study and 53 HBV WGS were generated for downstream analysis. Overall, 38% (22/57) and 62% (35/57) of patients had acute and chronic HBV infections, respectively. The prevalence of genotypes A, C, and D was 18.9% (10/53), 45.3% (24/53), and 35.8% (19/53), respectively. Among genotype A, C and D isolates subgenotype A1 (90%; 9/10), C1 (87.5%; 21/24) and D2 (78.9%; 15/19) predominates. The acute infection, virulence associated mutations, and viral load was higher in the genotype D isolates. Evidence of recombination was identified in 22.6% (12/53) of the HBV isolates including 20.0% (2/10), and 16.7% (4/24) and 31.6% (6/19) of genotype A, C and D isolates, respectively. The prevalence of recombination was higher in chronic HVB patients (32.2%; 10/31 versus 9.1%; 2/22); p<0.05. NAr mutations were identified in 47.2% (25/53) of the isolates including 33.9% novel mutations (18/53). HBV genotype C and D predominated in this population in Bangladesh; a comparatively high prevalence of recombinant HBV are circulating in this setting.

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.

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.

Climatic factors influencing dengue cases in Dhaka city: a model for dengue prediction.

BACKGROUND & OBJECTIVES: Transmission of dengue virus depends on the presence of Aedes mosquito. Mosquito generation and development is known to be influenced by the climate. This study was carried out to examine whether the climatic factors data can be used to predict yearly dengue cases of Dhaka city, Bangladesh. METHODS: Monthly reported dengue cases and climate data for the years 2000-2008 were obtained from the Directorate General of Health Services (DGHS) and Meteorological Department of Dhaka, Bangladesh, respectively. Data for the period 2000 to 2007 were used for development of a model through multiple linear regressions. Retrospective validation of the model was done with 2001, 2003, 2005 and 2008 data. Log transformation of the dependent variable was done to normalize data for linear regression. Average monthly humidity, rainfall, minimum and maximum temperature were used as independent variables and number of dengue cases reported monthly was used as dependent variable. Accuracy of the model for predicting outbreak was assessed through receiver operative characteristics (ROC) curve. RESULTS: Climatic factors, i.e. rainfall, maximum temperature and relative humidity were significantly correlated with monthly reported dengue cases. The model incorporating climatic data of two-lag month explained 61 per cent of variation in number of reported dengue cases and this model was found to predict dengue outbreak (≥ 200 cases) with considerable accuracy [area under ROC curve = 0.89, 95%CI = (0.89-0.98)]. INTERPRETATION & CONCLUSIONS: Our results showed that the climate had a major effect on the occurrence of dengue infection in Dhaka city. Though the prediction model had some limitations in predicting the monthly number of dengue cases, it could forecast possible outbreak two months in advance with considerable accuracy.