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1.
Medicina (Kaunas) ; 59(7)2023 Jul 10.
Article in English | MEDLINE | ID: mdl-37512091

ABSTRACT

Background and Objectives: The morbidity and mortality associated with COVID-19 have burdened worldwide healthcare systems beyond their capacities, forcing them to promptly investigate the virus characteristics and its associated outcomes. This clinical analysis aimed to explore the key factors related to the fatal outcome of severe COVID-19 cases. Materials and Methods: Thirty-five adult severe COVID-19 patients were enrolled from two COVID-19 hospitals in Dhaka, Bangladesh. Clinical manifestation, comorbid conditions, medications, SARS-CoV-2 RT-PCR related cycle threshold (CT) value, hematology, biochemical parameters with SARS-CoV-2 specific IgG and IgM responses at enrollment were compared between the survivors and deceased participants. Results: Total 27 patients survived and 8 patients died within 3 months of disease onset. Deceased patients suffered longer from shortness of breath than the survived (p = 0.049). Among the severe cases, 62% of the deceased patients had multiple comorbid condition compared to 48% of those who survived. Interestingly, the anti-viral was initiated earlier among the deceased patients [median day of 1 (IQR: 0, 1.5) versus 6.5 (IQR: 6.25, 6.75)]. Most of the survivors (55%) received a combination of anticoagulant (p = 0.034). Liver enzymes, creatinine kinase, and procalcitonin were higher among the deceased patients during enrollment. The median CT value among the deceased was significantly lower than the survivors (p = 0.025). A significant difference for initial IgG (p = 0.013) and IgM (p = 0.030) responses was found between the survivor and the deceased groups. Conclusions: The factors including older age, male gender, early onset of respiratory distress, multiple comorbidities, low CT value, and poor antibody response may contribute to the fatal outcome in severe COVID-19 patients. Early initiation of anti-viral and a combination of anticoagulant treatment may prevent or lower the fatality among severe COVID-19 cases.


Subject(s)
COVID-19 , Adult , Humans , Male , SARS-CoV-2 , Prospective Studies , Bangladesh/epidemiology , Antiviral Agents , Anticoagulants , Immunoglobulin G , Immunoglobulin M
2.
Clin Infect Dis ; 71(7): 1635-1642, 2020 10 23.
Article in English | MEDLINE | ID: mdl-31891368

ABSTRACT

BACKGROUND: Despite advances in prevention, detection, and treatment, cholera remains a major public health problem in Bangladesh and little is known about cholera outside of limited historical sentinel surveillance sites. In Bangladesh, a comprehensive national cholera control plan is essential, although national data are needed to better understand the magnitude and geographic distribution of cholera. METHODS: We conducted systematic hospital-based cholera surveillance among diarrhea patients in 22 sites throughout Bangladesh from 2014 to 2018. Stool specimens were collected and tested for Vibrio cholerae by microbiological culture. Participants' socioeconomic status and clinical, sanitation, and food history were recorded. We used generalized estimating equations to identify the factors associated with cholera among diarrhea patients. RESULTS: Among 26 221 diarrhea patients enrolled, 6.2% (n = 1604) cases were V. cholerae O1. The proportion of diarrhea patients positive for cholera in children <5 years was 2.1% and in patients ≥5 years was 9.5%. The proportion of cholera in Dhaka and Chittagong Division was consistently high. We observed biannual seasonal peaks (pre- and postmonsoon) for cholera across the country, with higher cholera positivity during the postmonsoon in western regions and during the pre-monsoon season in eastern regions. Cholera risk increased with age, occupation, and recent history of diarrhea among household members. CONCLUSIONS: Cholera occurs throughout a large part of Bangladesh. Cholera-prone areas should be prioritized to control the disease by implementation of targeted interventions. These findings can help strengthen the cholera-control program and serve as the basis for future studies for tracking the impact of cholera-control interventions in Bangladesh.


Subject(s)
Cholera , Vibrio cholerae , Bangladesh/epidemiology , Child , Cholera/epidemiology , Diarrhea/epidemiology , Hospitals , Humans
3.
J Med Virol ; 90(2): 383-387, 2018 02.
Article in English | MEDLINE | ID: mdl-28960396

ABSTRACT

The prevalence of hepatitis C virus (HCV) and genotypes among 965 individuals attending an HIV testing and counseling unit in Dhaka Bangladesh during Jan-Dec 2011 was determined. Anti-HCV antibody was detected in 4.4% individuals; the highest rate 37.8% was in people who inject drugs (PWID) followed by that in the general population (1.3%) and less than 1% in other populations. HCV RNA was detected in 2.7%. The most common genotype was genotype 3 (88.5%) followed by genotype 1 (11.5%). A national wide surveillance for HCV infection reaching all key populations is required to assess the countywide burden and to develop appropriate treatment strategies.


Subject(s)
HIV Infections/complications , Hepatitis C/epidemiology , Adult , Bangladesh/epidemiology , Female , Genotype , Hepacivirus/classification , Hepacivirus/genetics , Hepatitis C Antibodies/blood , Humans , Male , Prevalence , RNA, Viral/blood
4.
J Med Virol ; 90(4): 677-684, 2018 04.
Article in English | MEDLINE | ID: mdl-29244212

ABSTRACT

Human adenoviruses (HAdVs) are common cause of nonbacterial acute gastroenteritis worldwide. Limited data exist on HAdVs molecular epidemiology associated with acute gastroenteritis in Bangladesh. We describe the genetic diversity and epidemiology of HAdVs among hospitalized diarrhea patients, including HAdV genotypes, clinical symptoms, and co-infecting enteric pathogens. Stool samples were collected from ongoing diarrhea surveillance during 2012-2015. HAdV was detected using PCR and genotyped by sequencing and phylogenetic analysis. Detailed socio-demographic and clinical information regarding each individual was recorded such as duration of diarrhea, dehydration status, vomiting, abdominal pain, fever, and severity. Of 871 fecal specimens, HAdV DNA was detected in 93 (10.7%). Among them 56% were co-infected with other known enteric viral and bacterial pathogens and 31.6% had severe gastroenteritis. The majority (55%) of HAdV positives were children <5 years of age. Two main clinical symptoms in HAdV infected patients were diarrhea and vomiting. HAdVs were detected throughout the year with low prevalence in winter (November-January). Five HAdV species (A, B, C, D, and F) including 17 different genotypes were identified during the study period, with enteric HAdV species F (HAdV-40/41) being the most dominant. However, non-enteric HAdV were also detected in substantial proportion of specimens (15% species C, 15% species D, 10.8% species A, and 4.3% species B). Our study demonstrates high genetic diversity of HAdVs including enteric and non-enteric HAdVs among diarrhea patients and provides a foundation for further clarification of the role of non-enteric HAdVs in diarrheal diseases.


Subject(s)
Adenovirus Infections, Human/epidemiology , Adenovirus Infections, Human/virology , Adenoviruses, Human/classification , Adenoviruses, Human/isolation & purification , Gastroenteritis/epidemiology , Gastroenteritis/virology , Genotype , Adenovirus Infections, Human/pathology , Adenoviruses, Human/genetics , Adolescent , Adult , Aged , Bangladesh/epidemiology , Child , Child, Preschool , Coinfection/epidemiology , Coinfection/pathology , Coinfection/virology , Feces/virology , Female , Gastroenteritis/pathology , Genetic Variation , Humans , Infant , Male , Middle Aged , Molecular Epidemiology , Phylogeny , Polymerase Chain Reaction , Prevalence , Sequence Analysis, DNA , Young Adult
5.
BMC Infect Dis ; 14: 435, 2014 Aug 07.
Article in English | MEDLINE | ID: mdl-25098316

ABSTRACT

BACKGROUND: The study aimed to compare the socio-demographic, host and clinical characteristics, seasonality and antimicrobial susceptibility of Typhoidal Salmonella (Salmonella enterica serovar Typhi and Paratyphi) (TS) with diarrhea between urban and rural Bangladesh. METHODS: Relevant information of 77/25,767 (0.30%) and 290/17,622 (1.65%) patients positive with TS (in stool) were extracted from the data archive of Diarrheal Disease Surveillance System of icddr,b (urban Dhaka and rural Matlab Hospitals respectively) during 2000-2012. Comparison group (diarrhea patients negative for TS) was randomly selected from the database (1:3 ratio). Two poisson regression models were investigated for modelling seasonal effects on the number of cases. RESULTS: Salmonella Typhi was more frequently isolated in Dhaka than Matlab (57% vs. 5%, p < 0.001); while Salmonella Paratyphi was more frequent in Matlab than Dhaka (96% vs. 43%; p < 0.001). Fever [adj. OR-5.86 (95% CI: 2.16, 15.94)], antimicrobial use at home [5.08 (2.60, 9.90)], and fecal red blood cells [2.53 (1.38, 4.64)] were significantly associated with detection of TS in stool of patient from Dhaka. For Matlab, the correlates were, vomiting [1.88 (1.35, 2.64)], fecal macrophage [1.89 (1.29, 2.74)] in addition to fever and duration of diarrhea and antimicrobial use. At Dhaka, all Salmonella Typhi isolates were susceptible to ceftriaxone; while in Dhaka and Matlab however, for ciprofloxacin it was 45% and 91%, respectively. Susceptibility to chloramphenicol, ampicillin, trimethoprim-sulphamethoxazole and nalidixic acid ranged from 12%-58%. Salmonella Paratyphi were susceptible to ceftriaxone (99%). A significant seasonal trend and year difference (before and after 2007) for Matlab was observed (p < 0.001 for all effects). Dhaka does not show significant year or seasonal effects (p = 0.07 for years and p = 0.81 and p = 0.18 for the cos and sin components, respectively). While not significant, two seasonal peaks were observed in Dhaka (January-February and September-November); while a single peak (August-November) was observed in Matlab. CONCLUSIONS: Proportion of serovar distribution of TS and their clinical characteristics, antimicrobial susceptibility and seasonal pattern were different among diarrhea patients in urban Dhaka and rural Matlab of Bangladesh.


Subject(s)
Diarrhea/microbiology , Gastroenteritis/microbiology , Salmonella typhi/isolation & purification , Adolescent , Adult , Anti-Bacterial Agents/pharmacology , Bangladesh/epidemiology , Child , Child, Preschool , Diarrhea/epidemiology , Female , Gastroenteritis/epidemiology , Hospitals , Humans , Infant , Male , Microbial Sensitivity Tests , Middle Aged , Rural Health , Salmonella/classification , Salmonella/drug effects , Salmonella/genetics , Salmonella/isolation & purification , Salmonella typhi/classification , Salmonella typhi/drug effects , Salmonella typhi/genetics , Urban Health , Young Adult
6.
Microbiol Resour Announc ; 13(6): e0013524, 2024 Jun 11.
Article in English | MEDLINE | ID: mdl-38656213

ABSTRACT

We report 18 coding-complete genome sequences of emerging SARS-CoV-2 Omicron sub-lineages JN.1, JN.1.4, and JN.1.11 from Bangladesh. Nasopharyngeal swab samples were obtained from individuals with COVID-19 symptoms between December 2023 and January 2024. Whole genome sequencing was performed following the ARTIC Network-based protocol using Oxford Nanopore Technology.

7.
PLoS One ; 19(10): e0311993, 2024.
Article in English | MEDLINE | ID: mdl-39418288

ABSTRACT

BACKGROUND: The widespread increase in multiple variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) since 2020 is causing significant health concerns worldwide. While whole-genome sequencing (WGS) has played a leading role in surveillance programs, many local laboratories lack the expertise and resources. Thus, we aimed to investigate the circulating SARS-CoV-2 variants and evaluate the performance of multiplexed real-time reverse transcription-PCR (RT-PCR) for screening and monitoring the emergence of new SARS-CoV-2 variants in Bangladesh. METHODS: A total of 600 confirmed SARS-CoV-2-positive cases were enrolled either prospectively or retrospectively from two divisions of Bangladesh. The samples were screened by variant RT-PCR targeting five mutations of the spike gene (N501Y, P681R, L452R, E484K, E484Q). A subsample of the study population was also selected for third-generation sequencing (TGS) and the results were compared to the variant RT-PCR screening. An in-depth comparison was made between the two methods in terms of congruence and cost-benefit. RESULT: Seven variants were detected among samples, with similar distributions of the variants across both divisions. Variant RT-PCR for the targeted mutations lead to a 98.5% call rate; only nine samples failed to be determined. No association was found regarding the demographic features, clinical criteria, or routine RT-PCR Ct values across the variants. The clade diversity of the sequenced subpopulation (n = 99) exhibited similar distributions across the two study sites and other epidemiologic variables. Variant RT-PCR successfully distinguished variants of concern (VOCs) and variants of interest (VOIs); however, 8% discrepancy was observed for the closest lineages. Moreover, the variant RT-PCR represented an ideal balance of cost, time, and accuracy that outweigh their limitations. CONCLUSION: Based on the strong agreement of variant RT-PCR with TGS, such rapid, easily accessible approaches of rapid strain typing are essential in the context of pandemic responses to guide both treatment decisions and public health measures.


Subject(s)
COVID-19 , SARS-CoV-2 , Bangladesh/epidemiology , Humans , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , COVID-19/virology , COVID-19/diagnosis , Female , Male , Mutation , Adult , High-Throughput Nucleotide Sequencing/methods , Real-Time Polymerase Chain Reaction/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , Middle Aged , Retrospective Studies , Whole Genome Sequencing/methods , COVID-19 Nucleic Acid Testing/methods , Spike Glycoprotein, Coronavirus/genetics , Prospective Studies
8.
Virus Genes ; 46(3): 538-41, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23456827

ABSTRACT

We identified a novel inter-genotype recombinant norovirus strain, Dhaka85/2011/BGD, collected from a stool specimen of a nine-month-old infant who was hospitalized with diarrhea. Molecular investigation and phylogenetic analysis classified its RNA polymerase gene as GII.4-like, which commonly circulates in humans. The capsid gene was classified as GII.21-like, most likely originated from water. The discovery of this novel strain is an illustration of the enormous diversity among the norovirus strains, especially in developing countries and has important implications for future vaccine strategies.


Subject(s)
Norovirus/classification , Norovirus/genetics , Recombination, Genetic , Bangladesh , Caliciviridae Infections/virology , Capsid Proteins/genetics , Cluster Analysis , DNA-Directed RNA Polymerases/genetics , Feces/virology , Gastroenteritis/virology , Humans , Infant , Male , Molecular Sequence Data , Norovirus/isolation & purification , Phylogeny , RNA, Viral/genetics , Sequence Analysis, DNA
9.
BMC Infect Dis ; 13: 320, 2013 Jul 15.
Article in English | MEDLINE | ID: mdl-23855423

ABSTRACT

BACKGROUND: Rotavirus is the leading cause of severe diarrhea in infants and young children worldwide including Bangladesh. Unlike what was seen in high-income countries, the licensed rotavirus vaccines did not show high efficacy in Bangladeshi trials. We assessed rotavirus prevalence and genotypes in Bangladesh over six-year period to provide baseline information on the rotavirus burden and changing profile in the country. METHODS: This study was conducted from June 2006 to May 2012 in Matlab, Bangladesh. Group A rotaviruses were detected in stools collected from diarrhea patients by ELISA and genotyped using multiplex reverse transcription PCR followed by nucleotide sequencing. RESULTS: Of the 9678 stool samples, 20.3% were positive for rotavirus. The most predominant genotype was G1P[8] (22.4%), followed by G9P[8] (20.8%), G2P[4] (16.9%) and G12P[8] (10.4%). Mixed infections were detected in 14.2% of the samples. Emergence of an unusual strain, G9P[4] was documented during 2011-12. Several amino acid mismatches in the antigenic epitopes of VP7 and VP4 between Bangladeshi and the vaccine strains were identified. CONCLUSIONS: Our study provides important information on rotavirus genotypes that should be considered for the selection and introduction of rotavirus vaccines in Bangladesh.


Subject(s)
Rotavirus Infections/virology , Rotavirus/genetics , Amino Acid Sequence , Amino Acid Substitution , Antigens, Viral/immunology , Bangladesh/epidemiology , Diarrhea/epidemiology , Diarrhea/virology , Feces/virology , Genotype , Humans , Molecular Sequence Data , Prospective Studies , Rotavirus/immunology , Rotavirus/isolation & purification , Rotavirus Infections/epidemiology , Rotavirus Vaccines/administration & dosage , Rotavirus Vaccines/immunology
10.
Microbiol Resour Announc ; 12(3): e0000123, 2023 Mar 16.
Article in English | MEDLINE | ID: mdl-36779717

ABSTRACT

Here, we report the coding-complete genome sequences of 40 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains of the newly emerged recombinant Omicron variants XBB, XBB.1, and XBB.2. The strains were isolated from nasopharyngeal swab samples that had been collected from symptomatic patients in Bangladesh between September and October 2022 and were sequenced using an Oxford Nanopore Technologies (ONT) system.

11.
Nat Commun ; 14(1): 3773, 2023 06 24.
Article in English | MEDLINE | ID: mdl-37355673

ABSTRACT

Ongoing diarrheal disease surveillance throughout Bangladesh over the last decade has revealed seasonal localised cholera outbreaks in Cox's Bazar, where both Bangladeshi Nationals and Forcibly Displaced Myanmar Nationals (FDMNs) reside in densely populated settlements. FDMNs were recently targeted for the largest cholera vaccination campaign in decades. We aimed to infer the epidemic risk of circulating Vibrio cholerae strains by determining if isolates linked to the ongoing global cholera pandemic ("7PET" lineage) were responsible for outbreaks in Cox's Bazar. We found two sublineages of 7PET in this setting during the study period; one with global distribution, and a second lineage restricted to Asia and the Middle East. These subclades were associated with different disease patterns that could be partially explained by genomic differences. Here we show that as the pandemic V. cholerae lineage circulates in this vulnerable population, without a vaccine intervention, the risk of an epidemic was very high.


Subject(s)
Cholera , Vibrio cholerae , Humans , Vibrio cholerae/genetics , Cholera/epidemiology , Cholera/prevention & control , Bangladesh/epidemiology , Genomics , Immunization Programs , Pandemics
12.
Microbiol Resour Announc ; 12(10): e0056223, 2023 Oct 19.
Article in English | MEDLINE | ID: mdl-37668364

ABSTRACT

We announce the coding-complete genomes of four different strains of SARS-CoV-2 Omicron lineages, XBB.1.16, XBB.2.3, FL.4 (alias of XBB.1.9.1.4), and XBB.3. These strains were obtained between October 2022 and May 2023 from nasopharyngeal swabs of four Bangladeshi individuals, while one of them had a travel history. Genomic data were produced by implementing ARTIC Network-based amplicon sequencing using the Oxford Nanopore Technology.

13.
Front Genet ; 14: 1220906, 2023.
Article in English | MEDLINE | ID: mdl-37621704

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to give rise to a highly transmissive and immune-escaping variant of concern, known as Omicron. Many aspects of the evolution of SARS-CoV-2 and the driving forces behind the ongoing Omicron outbreaks remain unclear. Substitution at the receptor-binding domain (RBD) in the spike protein is one of the primary strategies of SARS-CoV-2 Omicron to hinder recognition by the host angiotensin-converting enzyme 2 (ACE2) receptor and avoid antibody-dependent defense activation. Here, we scanned for adaptive evolution within the SARS-CoV-2 Omicron genomes reported from Bangladesh in the public database GISAID (www.gisaid.org; dated 2 April 2023). The ratio of the non-synonymous (Ka) to synonymous (Ks) nucleotide substitution rate, denoted as ω, is an indicator of the selection pressure acting on protein-coding genes. A higher proportion of non-synonymous to synonymous substitutions (Ka/Ks or ω > 1) indicates positive selection, while Ka/Ks or ω near zero indicates purifying selection. An equal amount of non-synonymous and synonymous substitutions (Ka/Ks or ω = 1) refers to neutrally evolving sites. We found evidence of adaptive evolution within the spike (S) gene of SARS-CoV-2 Omicron isolated from Bangladesh. In total, 22 codon sites of the S gene displayed a signature of positive selection. The data also highlighted that the receptor-binding motif within the RBD of the spike glycoprotein is a hotspot of adaptive evolution, where many of the codons had ω > 1. Some of these adaptive sites at the RBD of the spike protein are known to be associated with increased viral fitness. The M gene and ORF6 have also experienced positive selection. These results suggest that although purifying selection is the dominant evolutionary force, positive Darwinian selection also plays a vital role in shaping the evolution of SARS-CoV-2 Omicron in Bangladesh.

14.
Front Public Health ; 11: 1132927, 2023.
Article in English | MEDLINE | ID: mdl-37124777

ABSTRACT

Background: Enterotoxigenic Escherichia coli (ETEC) and Vibrio cholerae O1 are most common bacterial causes of diarrheal diseases in Bangladesh. This analysis projected distribution of ETEC and V. cholerae O1 among diarrheal patients of icddr,b, Dhaka hospital in two diarrheal peaks of 2022. Methodology: Under the 2% systematic surveillance system, stool samples collected from diarrheal patients of icddr,b hospital were cultured and diagnostic testing was done for ETEC and V. cholerae O1. Comparison of positive cases was done between first peak (March-April) and second peak (October-November) in 2022. Results: A total of 2,937 stool specimens were tested of which 12% were ETEC and 20% were V. cholerae O1. About 40% of the severe dehydration cases were infected with V. cholerae O1. Predominant ETEC enterotoxin type was 'LT/ST' (41%). The LT enterotoxin significantly increased from 13% to 28% in the second peak (p = 0.015). The predominant colonization factors (CFs) on ETEC were CS5 + CS6 (23%), followed by CS6 (15%). CF-positive isolates was significantly higher in the second peak (36%) than in the first peak (22%) (p = 0.043). Total 14% cases were co-infected with ETEC and V. cholerae O1. Significant differences in the distribution of enterotoxin types were observed (p = 0.029) among the co-infection cases. Conclusion: Changing patterns of enterotoxin and CFs observed in ETEC pathogens should be taken into consideration for ETEC vaccine development. Considering cholera and ETEC biannual trends in causing diarrheal epidemics and outbreaks, emphasizes the need for thoughts on combination vaccine strategies for preventing acute watery diarrhea due to the two major bacterial pathogens.


Subject(s)
Enterotoxigenic Escherichia coli , Epidemics , Escherichia coli Infections , Vibrio cholerae O1 , Humans , Escherichia coli Infections/epidemiology , Escherichia coli Infections/microbiology , Bangladesh/epidemiology , Diarrhea/epidemiology , Enterotoxins
15.
Am J Trop Med Hyg ; 109(3): 575-583, 2023 09 06.
Article in English | MEDLINE | ID: mdl-37580033

ABSTRACT

Despite focusing on cholera burden, epidemiologic studies in Bangladesh tend to be limited in geographic scope. National-level cholera surveillance data can help inform cholera control strategies and assess the effectiveness of preventive measures. Hospital-based sentinel surveillance among patients with suspected diarrhea in different sites across Bangladesh has been conducted since 2014. We selected an age-stratified sample of 20 suspected cholera cases each week from each sentinel site, tested stool for the presence of Vibrio cholerae O1/O139 by culture, and characterized antibiotic susceptibility in a subset of culture-positive isolates. We estimated the odds of being culture positive among suspected cholera cases according to different potential risk factors. From May 4, 2014 through November 30, 2021, we enrolled 51,414 suspected cases from our sentinel surveillance sites. We confirmed V. cholerae O1 in 5.2% of suspected cases through microbiological culture. The highest proportion of confirmed cholera cases was from Chittagong (9.7%) and the lowest was from Rangpur Division (0.9%). Age, number of purges, duration of diarrhea, occupation, and season were the most relevant factors in distinguishing cholera-positive suspected cases from cholera-negative suspected cases. Nationwide surveillance data show that cholera is circulating in Bangladesh and the southern region is more affected than the northern region. Antimicrobial resistance patterns indicate that multidrug resistance (resistance to three or more classes of antibiotics) of V. cholerae O1 could be a major threat in the future. Alignment of these results with Bangladesh's cholera-control program will be the foundation for future research into the efficacy of cholera-control initiatives.


Subject(s)
Cholera , Vibrio cholerae O1 , Humans , Infant , Cholera/epidemiology , Cholera/microbiology , Sentinel Surveillance , Bangladesh/epidemiology , Disease Outbreaks , Diarrhea/epidemiology , Diarrhea/microbiology
16.
Microbiol Resour Announc ; 12(1): e0095022, 2023 Jan 24.
Article in English | MEDLINE | ID: mdl-36472422

ABSTRACT

We announce the coding-complete genome sequences of 23 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron strains obtained from Bangladeshi individuals. The Oxford Nanopore Technologies sequencing platform was utilized to generate the genomic data, deploying ARTIC Network-based amplicon sequencing.

17.
J Clin Microbiol ; 50(3): 837-40, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22205790

ABSTRACT

Confirmative diagnosis of visceral leishmaniasis (VL) is still a challenge at the primary health care facilities in most of the rural areas of endemicity in the Indian subcontinent. Conventional methods for parasitological confirmation are risky and require skilled personnel, and hence they are unavailable to the poor people in the regions of endemicity. Buffy coat smear microscopy, as a minimally invasive, simple alternative for the parasitological diagnosis of VL, was evaluated in this prospective study. One hundred twelve VL patients were enrolled in this study. The buffy coat was separated from peripheral blood of all enrolled subjects using Histopaque-1119 solution. Leishman-stained buffy coat smears were examined for Leishmania donovani bodies, and buffy coat was also utilized for detection of parasite DNA by Leishmania nested PCR (LnPCR) for all cases. Concomitant splenic smears could be examined for L. donovani bodies in 66 cases, and the parasite load was graded on a scale of 1+ to 6+ for L. donovani-positive smears. All splenic smear-positive cases were also found to be positive by LnPCR. Of 112 enrolled VL cases, 103 (92%) were found to be positive for L. donovani bodies in buffy coat smear microscopy, which is promising as a confirmative diagnosis tool. We have also found a significant association of the buffy coat smear positivity with parasitic burden in the spleen smear. In this preliminary observation in Bangladesh, buffy coat smear microscopy has been found to be very simple, minimally invasive, and risk-free method of parasitological diagnosis of VL with a good diagnostic accuracy and potential for field use.


Subject(s)
Blood Buffy Coat/parasitology , Clinical Laboratory Techniques/methods , Leishmania donovani/cytology , Leishmaniasis, Visceral/diagnosis , Microscopy/methods , Parasitology/methods , Adolescent , Adult , Bangladesh , Child , DNA, Protozoan/genetics , DNA, Protozoan/isolation & purification , Female , Humans , Leishmania donovani/genetics , Male , Polymerase Chain Reaction/methods , Prospective Studies , Young Adult
18.
Am J Trop Med Hyg ; 107(4): 845-849, 2022 10 12.
Article in English | MEDLINE | ID: mdl-35970285

ABSTRACT

Early detection of SARS-CoV-2 infection is crucial to prevent its spread. This study aimed to document test sensitivity/specificity, correlation with cycle threshold value from polymerase chain reaction (PCR), fitness-for-use in different populations and settings, and user perspectives that could inform large-scale implementation. In this study, we evaluated the performance of a rapid antigen detection test, BD Veritor, and compared this (and another rapid test, Standard Q) against reverse transcription PCR (RT-PCR) in terms of sensitivity and specificity in 130 symptomatic and 130 asymptomatic adults. In addition, we evaluated the suitability and ease of use of the BD Veritor test in a subsample of study participants (n = 42) and implementers (n = 5). At 95% confidence interval, the sensitivity of the BD Veritor and Standard Q test were 70% and 63% in symptomatic and 87% and 73% in asymptomatic individuals, respectively, regarding positive SARS-CoV-2 RT-PCR results. Overall, the BD Veritor test was 78% sensitive and 99.5% specific compared with RT-PCR irrespective of the cycle threshold. This warrants large field evaluation as well as use of the rapid antigen test for quick assessment of SARS-CoV-2 for containment of epidemics in the country.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , Antigens, Viral , Bangladesh/epidemiology , COVID-19/diagnosis , COVID-19 Testing , Humans , Sensitivity and Specificity
19.
Microbiol Resour Announc ; 11(4): e0011922, 2022 Apr 21.
Article in English | MEDLINE | ID: mdl-35323016

ABSTRACT

We report the coding-complete genome sequences of 25 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineage B.1.1.529 Omicron strains obtained from Bangladeshi individuals in samples collected between December 2021 and January 2022. Genomic data were generated by Nanopore sequencing using the amplicon sequencing approach developed by the ARTIC Network.

20.
PLoS Negl Trop Dis ; 16(1): e0010102, 2022 01.
Article in English | MEDLINE | ID: mdl-34982773

ABSTRACT

BACKGROUND: COVID-19 caused by SARS-CoV-2 ranges from asymptomatic to severe disease and can cause fatal and devastating outcome in many cases. In this study, we have compared the clinical, biochemical and immunological parameters across the different disease spectrum of COVID-19 in Bangladeshi patients. METHODOLOGY/PRINCIPAL FINDINGS: This longitudinal study was conducted in two COVID-19 hospitals and also around the community in Dhaka city in Bangladesh between November 2020 to March 2021. A total of 100 patients with COVID-19 infection were enrolled and classified into asymptomatic, mild, moderate and severe cases (n = 25/group). In addition, thirty age and sex matched healthy participants were enrolled and 21 were analyzed as controls based on exclusion criteria. After enrollment (study day1), follow-up visits were conducted on day 7, 14 and 28 for the cases. Older age, male gender and co-morbid conditions were the risk factors for severe COVID-19 disease. Those with moderate and severe cases of infection had low lymphocyte counts, high neutrophil counts along with a higher neutrophil-lymphocyte ratio (NLR) at enrollment; this decreased to normal range within 42 days after the onset of symptom. At enrollment, D-dimer, CRP and ferritin levels were elevated among moderate and severe cases. The mild, moderate, and severe cases were seropositive for IgG antibody by day 14 after enrollment. Moderate and severe cases showed significantly higher IgM and IgG levels of antibodies to SARS-CoV-2 compared to mild and asymptomatic cases. CONCLUSION/SIGNIFICANCE: We report on the clinical, biochemical, and hematological parameters associated with the different severity of COVID-19 infection. We also show different profile of antibody response against SARS-CoV-2 in relation to disease severity, especially in those with moderate and severe disease manifestations compared to the mild and asymptomatic infection.


Subject(s)
Antibodies, Viral/immunology , COVID-19/diagnosis , COVID-19/immunology , Severity of Illness Index , Adult , Antibody Formation , Bangladesh , COVID-19 Testing , Cohort Studies , Female , Fibrin Fibrinogen Degradation Products , Humans , Immunoglobulin G , Longitudinal Studies , Lymphocytes , Male , Middle Aged , Neutrophils , Risk Factors , SARS-CoV-2 , Viral Load
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