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1.
J Infect Dis ; 2024 Apr 29.
Article in English | MEDLINE | ID: mdl-38682164

ABSTRACT

BACKGROUND: Nipah virus (NiV), a highly lethal virus in humans, circulates in Pteropus bats throughout South and Southeast Asia. Difficulty in obtaining viral genomes from bats means we have a poor understanding of NiV diversity. METHODS: We develop phylogenetic approaches applied to the most comprehensive collection of genomes to date (N=257, 175 from bats, 73 from humans) from six countries over 22 years (1999-2020). We divide the four major NiV sublineages into 15 genetic clusters. Using Approximate Bayesian Computation fit to a spatial signature of viral diversity, we estimate the presence and the average size of genetic clusters per area. RESULTS: We find that, within any bat roost, there are an average of 2.4 co-circulating genetic clusters, rising to 5.5 clusters at areas of 1500-2000km2. We estimate that each genetic cluster occupies an average area of 1.3million km2 (95%CI: 0.6-2.3 million), with 14 clusters in an area of 100,000km2 (95%CI: 6-24). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most clusters have been identified, but only ∼15% of overall NiV diversity has been uncovered. CONCLUSION: Our findings are consistent with entrenched co-circulation of distinct lineages, even within roosts, coupled with slow migration over larger spatial scales.

2.
Hum Genomics ; 17(1): 58, 2023 Jul 07.
Article in English | MEDLINE | ID: mdl-37420264

ABSTRACT

BACKGROUND: Wastewater-based epidemiological surveillance has been considered a powerful tool for early detection and monitoring of the dynamics of SARS-CoV-2 and its lineages circulating in a community. This study is aimed to investigate the complexity of SARS-CoV-2 infection dynamics in Dhaka city by examining its genetic variants in wastewater. Also, the study seeks to determine a connection between the SARS-CoV-2 variations detected in clinical testing and those found in wastewater samples. RESULTS: Out of 504 samples tested in RT-qPCR, 185 (36.7%) tested positive for SARS-CoV-2 viral RNA. The median log10 concentration of SARS-CoV-2 N gene copies/Liter of wastewater (gc/L) was 5.2, and the median log10 concentration of ORF1ab was 4.9. To further reveal the genetic diversity of SARS-CoV-2, ten samples with ORF1ab real-time RT-PCR cycle threshold (Ct) values ranging from 28.78 to 32.13 were subjected to whole genome sequencing using nanopore technology. According to clade classification, sequences from wastewater samples were grouped into 4 clades: 20A, 20B, 21A, 21J, and the Pango lineage, B.1, B.1.1, B.1.1.25, and B.1.617.2, with coverage ranging from 94.2 to 99.8%. Of them, 70% belonged to clade 20B, followed by 10% to clade 20A, 21A, and 21J. Lineage B.1.1.25 was predominant in Bangladesh and phylogenetically related to the sequences from India, the USA, Canada, the UK, and Italy. The Delta variant (B.1.617.2) was first identified in clinical samples at the beginning of May 2021. In contrast, we found that it was circulating in the community and was detected in wastewater in September 2020. CONCLUSION: Environmental surveillance is useful for monitoring temporal and spatial trends of existing and emerging infectious diseases and supports evidence-based public health measures. The findings of this study supported the use of wastewater-based epidemiology and provided the baseline data for the dynamics of SARS-CoV-2 variants in the wastewater environment in Dhaka, Bangladesh.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Bangladesh/epidemiology , COVID-19/epidemiology , Public Health Surveillance , Wastewater , Complement System Proteins , RNA
3.
Emerg Infect Dis ; 29(2): 393-396, 2023 02.
Article in English | MEDLINE | ID: mdl-36692447

ABSTRACT

Spillovers of Nipah virus (NiV) from Pteropus bats to humans occurs frequently in Bangladesh, but the risk for spillover into other animals is poorly understood. We detected NiV antibodies in cattle, dogs, and cats from 6 sites where spillover human NiV infection cases occurred during 2013-2015.


Subject(s)
Chiroptera , Henipavirus Infections , Nipah Virus , Humans , Animals , Dogs , Cattle , Bangladesh/epidemiology , Henipavirus Infections/epidemiology , Henipavirus Infections/veterinary , Disease Outbreaks
4.
Emerg Infect Dis ; 28(7): 1384-1392, 2022 07.
Article in English | MEDLINE | ID: mdl-35731130

ABSTRACT

Knowledge of the dynamics and genetic diversity of Nipah virus circulating in bats and at the human-animal interface is limited by current sampling efforts, which produce few detections of viral RNA. We report a series of investigations at Pteropus medius bat roosts identified near the locations of human Nipah cases in Bangladesh during 2012-2019. Pooled bat urine was collected from 23 roosts; 7 roosts (30%) had >1 sample in which Nipah RNA was detected from the first visit. In subsequent visits to these 7 roosts, RNA was detected in bat urine up to 52 days after the presumed exposure of the human case-patient, although the probability of detection declined rapidly with time. These results suggest that rapidly deployed investigations of Nipah virus shedding from bat roosts near human cases could increase the success of viral sequencing compared with background surveillance and could enhance understanding of Nipah virus ecology and evolution.


Subject(s)
Chiroptera , Henipavirus Infections , Nipah Virus , Animals , Bangladesh/epidemiology , Henipavirus Infections/epidemiology , Henipavirus Infections/veterinary , Humans , Nipah Virus/genetics , RNA, Viral/genetics
5.
J Clin Lab Anal ; 36(2): e24203, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34942043

ABSTRACT

BACKGROUND: Globally, real-time reverse transcription-polymerase chain reaction (rRT-PCR) is the reference detection technique for SARS-CoV-2, which is expensive, time consuming, and requires trained laboratory personnel. Thus, a cost-effective, rapid antigen test is urgently needed. This study evaluated the performance of the rapid antigen tests (RATs) for SARS-CoV-2 compared with rRT-PCR, considering different influencing factors. METHODS: We enrolled a total of 214 symptomatic individuals with known COVID-19 status using rRT-PCR. We collected and tested paired nasopharyngeal (NP) and nasal swab (NS) specimens (collected from same individual) using rRT-PCR and RATs (InTec and SD Biosensor). We assessed the performance of RATs considering specimen types, viral load, the onset of symptoms, and presenting symptoms. RESULTS: We included 214 paired specimens (112 NP and 100 NS SARS-CoV-2 rRT-PCR positive) to the analysis. For NP specimens, the average sensitivity, specificity, and accuracy of the RATs were 87.5%, 98.6%, and 92.8%, respectively, when compared with rRT-PCR. While for NS, the overall kit performance was slightly lower than that of NP (sensitivity 79.0%, specificity 96.1%, and accuracy 88.3%). We observed a progressive decline in the performance of RATs with increased Ct values (decreased viral load). Moreover, the RAT sensitivity using NP specimens decreased over the time of the onset of symptoms. CONCLUSION: The RATs showed strong performance under field conditions and fulfilled the minimum performance limit for rapid antigen detection kits recommended by World Health Organization. The best performance of the RATs can be achieved within the first week of the onset of symptoms with high viral load.


Subject(s)
Antigens, Viral/analysis , COVID-19 Serological Testing , COVID-19/diagnosis , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19 Serological Testing/methods , COVID-19 Serological Testing/standards , COVID-19 Serological Testing/statistics & numerical data , Child , Child, Preschool , Female , Humans , Infant , Male , Middle Aged , Nasopharynx/virology , Reagent Kits, Diagnostic/virology , SARS-CoV-2/isolation & purification , Sensitivity and Specificity , Time Factors , Viral Load , Young Adult
6.
J Infect Dis ; 224(12 Suppl 2): S864-S872, 2021 12 20.
Article in English | MEDLINE | ID: mdl-34586390

ABSTRACT

BACKGROUND: Since August 2017, Myanmar nationals from Rakhine state have crossed the border into Bangladesh and settled in Cox's Bazar, the World's largest refugee camp. Due to overcrowding, poor sanitation, and hygienic practices they have been under significant health risks including diarrheal diseases. The objective of this study is to determine the viral etiology of acute gastroenteritis (AGE) among forcibly displaced Myanmar nationals (FDMN) and adjacent Bangladeshi local host population (AHP). METHODS: From April 2018 to April 2019, we collected stool specimens from 764 FDMN and 1159 AHP of all ages. We tested 100 randomly selected specimens from each group for the most common AGE viruses. RESULTS: Among 200 diarrhea patients, 55% and 64% of FDMN and AHP patients, respectively, had viral infections; the most common viruses were rotavirus (29% vs 44%), adenovirus (24% vs 31%), and norovirus (14% vs 10%). In both populations, viral infections were significantly higher in children less than 5 years of age, compared with bacterial infections that were higher in patients older than 5 years of age (P ≤ .05). CONCLUSIONS: Disparities in viral and bacterial prevalence among various age groups warrant careful antibiotic usage, especially in children less than 5 years of age.


Subject(s)
Diarrhea/epidemiology , Feces/virology , Gastroenteritis/diagnosis , Gastroenteritis/virology , Refugees , Adenoviridae , Adolescent , Bangladesh/epidemiology , Child , Child, Preschool , Female , Gastroenteritis/ethnology , Humans , Infant , Male , Myanmar/ethnology , Norovirus , Prevalence , Reverse Transcriptase Polymerase Chain Reaction , Rotavirus
7.
Clin Infect Dis ; 69(3): 505-513, 2019 07 18.
Article in English | MEDLINE | ID: mdl-30351379

ABSTRACT

BACKGROUND: Noroviruses are the most common cause of epidemic and endemic acute gastroenteritis (AGE) worldwide. The burden of norovirus disease in low-income settings is poorly understood. METHODS: We tested stool samples from children less than 5 years of age with diarrhea who were admitted in a rural hospital in Bangladesh from 2010-2012 and from matched, healthy controls from the same catchment area. RESULTS: Norovirus was detected in 109 (18%) of 613 children with diarrhea and in 30 (15%) of 206 healthy controls. Most (n = 118; 85%) norovirus infections belonged to genogroup II (GII). Of these, GII.4 viruses were identified in 36 (33%) of the cases and in 6 (21%) of the controls. Other major genotypes included GII.3 (13%), GII.6 (11%), and GII.13 (11%) in the cases and GII.6 (17%) and GII.2 (14%) in the controls. The greatest risk of severe norovirus disease (Vesikari score ≥11) was associated with GII.4 infections. GII.4 viruses were the predominant genotype detected during the winter (55%) and rainy season (23%), while GII.3 (19%) and GII.13 (19%) viruses were the most prevalent genotypes during the summer. Vomiting was significantly associated with GII.4 infections, while longer durations of diarrhea were associated with GI.3 infections. CONCLUSIONS: Future studies are needed to understand the high rates of virus shedding in children without AGE symptoms.


Subject(s)
Caliciviridae Infections/epidemiology , Diarrhea/epidemiology , Feces/virology , Norovirus/genetics , Acute Disease , Bangladesh/epidemiology , Case-Control Studies , Child, Preschool , Cost of Illness , Diarrhea/virology , Female , Gastroenteritis/epidemiology , Gastroenteritis/virology , Genotype , Healthy Volunteers , Humans , Infant , Infant, Newborn , Male , Poverty/statistics & numerical data , Prevalence , RNA, Viral/genetics , Rural Population/statistics & numerical data , Seasons , Virus Shedding
8.
J Med Virol ; 91(4): 549-554, 2019 04.
Article in English | MEDLINE | ID: mdl-30372530

ABSTRACT

BACKGROUND: Acute respiratory infection (ARI) is a leading cause of morbidity and mortality in children in low and middle-income countries. Human metapneumovirus (hMPV) is one of the most common viral etiological agents for ARIs in children. OBJECTIVES: In this study, we explored the genotypic diversity and the epidemiology of hMPV among infants in Dhaka, Bangladesh. STUDY DESIGN: Between December 2014 and August 2016, a total of 3810 mid-turbinate nasal swab samples were collected from infants (0 to 6 months of age) who met clinical ARI criteria, as a part of a prospective ARI cohort study. hMPV was detected using polymerase chain reaction, and genotyped by sequencing and phylogenetic analysis. RESULTS: hMPV was identified in 206 (5.4%) nasal swab specimens. One-tenth of the hMPV-positive swabs (n = 19) were also positive for other respiratory viruses. hMPV activity peaked in January and September in 2015; however, no seasonal pattern of hMPV infection was detected. Phylogenetic analyses of the N and F gene-fragments revealed that the hMPV strains circulating in Dhaka, Bangladesh, belonged to three genotypes: A2b, A2c, and B1. Genotype A (57%) was the predominant hMPV genotype circulating in Bangladesh during the study period. CONCLUSION: This study describes both the epidemiology of hMPV infection and its genotypic strain diversity in Dhaka, Bangladesh.


Subject(s)
Genotype , Metapneumovirus/classification , Metapneumovirus/genetics , Paramyxoviridae Infections/epidemiology , Paramyxoviridae Infections/virology , Bangladesh/epidemiology , Community-Acquired Infections/epidemiology , Community-Acquired Infections/virology , Cross Infection/epidemiology , Cross Infection/virology , Epidemiological Monitoring , Genetic Variation , Genotyping Techniques , Humans , Infant , Infant, Newborn , Metapneumovirus/isolation & purification , Molecular Epidemiology , Nasal Mucosa/virology , Polymerase Chain Reaction , Prospective Studies , Sequence Analysis, DNA
9.
Emerg Infect Dis ; 24(5): 926-928, 2018 05.
Article in English | MEDLINE | ID: mdl-29664373

ABSTRACT

Dromedary camels are bred domestically and imported into Bangladesh. In 2015, of 55 camels tested for Middle East respiratory syndrome coronavirus in Dhaka, 17 (31%) were seropositive, including 1 bred locally. None were PCR positive. The potential for infected camels in urban markets could have public health implications and warrants further investigation.


Subject(s)
Camelus , Coronavirus Infections/veterinary , Middle East Respiratory Syndrome Coronavirus/isolation & purification , Animals , Bangladesh/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Female , Male
10.
Emerg Infect Dis ; 24(1): 15-21, 2018 01.
Article in English | MEDLINE | ID: mdl-29260663

ABSTRACT

Nipah virus (NiV) has been transmitted from patient to caregivers in Bangladesh presumably through oral secretions. We aimed to detect whether NiV-infected patients contaminate hospital surfaces with the virus. During December 2013-April 2014, we collected 1 swab sample from 5 surfaces near NiV-infected patients and tested surface and oral swab samples by real-time reverse transcription PCR for NiV RNA. We identified 16 Nipah patients; 12 cases were laboratory-confirmed and 4 probable. Of the 12 laboratory-confirmed cases, 10 showed NiV RNA in oral swab specimens. We obtained surface swab samples for 6 Nipah patients; 5 had evidence of NiV RNA on >1 surface: 4 patients contaminated towels, 3 bed sheets, and 1 the bed rail. Patients with NiV RNA in oral swab samples were significantly more likely than other Nipah patients to die. To reduce the risk for fomite transmission of NiV, infection control should target hospital surfaces.


Subject(s)
Equipment Contamination , Henipavirus Infections/epidemiology , Henipavirus Infections/virology , Hospitals , Nipah Virus/isolation & purification , Bangladesh/epidemiology , Bedding and Linens/virology , Beds/virology , Disease Outbreaks , Fomites , Henipavirus Infections/mortality , Humans , Infection Control/methods , Mouth/virology , RNA, Viral/isolation & purification
11.
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
13.
Clin Infect Dis ; 64(suppl_3): S378-S386, 2017 Jun 15.
Article in English | MEDLINE | ID: mdl-28575375

ABSTRACT

BACKGROUND.: Lack of a gold standard for identifying bacterial and viral etiologies of pneumonia has limited evaluation of C-reactive protein (CRP) for identifying bacterial pneumonia. We evaluated the sensitivity and specificity of CRP for identifying bacterial vs respiratory syncytial virus (RSV) pneumonia in the Pneumonia Etiology Research for Child Health (PERCH) multicenter case-control study. METHODS.: We measured serum CRP levels in cases with World Health Organization-defined severe or very severe pneumonia and a subset of community controls. We evaluated the sensitivity and specificity of elevated CRP for "confirmed" bacterial pneumonia (positive blood culture or positive lung aspirate or pleural fluid culture or polymerase chain reaction [PCR]) compared to "RSV pneumonia" (nasopharyngeal/oropharyngeal or induced sputum PCR-positive without confirmed/suspected bacterial pneumonia). Receiver operating characteristic (ROC) curves were constructed to assess the performance of elevated CRP in distinguishing these cases. RESULTS.: Among 601 human immunodeficiency virus (HIV)-negative tested controls, 3% had CRP ≥40 mg/L. Among 119 HIV-negative cases with confirmed bacterial pneumonia, 77% had CRP ≥40 mg/L compared with 17% of 556 RSV pneumonia cases. The ROC analysis produced an area under the curve of 0.87, indicating very good discrimination; a cut-point of 37.1 mg/L best discriminated confirmed bacterial pneumonia (sensitivity 77%) from RSV pneumonia (specificity 82%). CRP ≥100 mg/L substantially improved specificity over CRP ≥40 mg/L, though at a loss to sensitivity. CONCLUSIONS.: Elevated CRP was positively associated with confirmed bacterial pneumonia and negatively associated with RSV pneumonia in PERCH. CRP may be useful for distinguishing bacterial from RSV-associated pneumonia, although its role in discriminating against other respiratory viral-associated pneumonia needs further study.


Subject(s)
C-Reactive Protein/analysis , Pneumonia, Bacterial/diagnosis , Pneumonia, Viral/diagnosis , Bacteria/genetics , Bacteria/isolation & purification , Biomarkers/blood , Case-Control Studies , Child, Preschool , Community-Acquired Infections/diagnosis , Female , Humans , Infant , Infant, Newborn , Male , Nasopharynx/virology , Oropharynx/virology , Pneumonia, Bacterial/microbiology , Pneumonia, Viral/virology , Polymerase Chain Reaction , ROC Curve , Respiratory Syncytial Virus Infections/blood , Respiratory Syncytial Virus, Human/genetics , Respiratory Syncytial Virus, Human/isolation & purification , Sensitivity and Specificity
14.
BMC Pregnancy Childbirth ; 16(1): 309, 2016 10 13.
Article in English | MEDLINE | ID: mdl-27737646

ABSTRACT

BACKGROUND: Early infancy is a high-risk period for severe acute respiratory infection (ARI), particularly in low-income countries with resource-limited health systems. Lower respiratory tract infection (LRTI) is commonly preceded by upper respiratory infection (URTI), and often caused by respiratory syncytial virus (RSV), influenza and other common community-acquired viral pathogens. Vitamin D status is a candidate modifiable early-life determinant of the host antiviral immune response and thus may influence the risk of ARI-associated morbidity in high-risk populations. METHODS/DESIGN: In the Maternal Vitamin D for Infant Growth (MDIG) study in Dhaka, Bangladesh (NCT01924013), 1300 pregnant women are randomized to one of five groups: placebo, 4200 IU/week, 16,800 IU/week, or 28,000 IU/week from 2nd trimester to delivery plus placebo from 0-6 months postpartum; or, 28,000 IU/week prenatal and until 6-months postpartum. In the Maternal Vitamin D for ARI in Infancy (MDARI) sub-study nested within the MDIG trial, trained personnel conduct weekly postnatal home visits to inquire about ARI symptoms and conduct a standardized clinical assessment. Supplementary home visits between surveillance visits are conducted when caregivers make phone notifications of new infant symptoms. Mid-turbinate nasal swab samples are obtained from infants who meet standardized clinical ARI criteria. Specimens are tested by polymerase chain reaction (PCR) for 8 viruses (influenza A/B, parainfluenza 1/2/3, RSV, adenovirus, and human metapneumovirus), and nasal carriage density of Streptococcus pneumoniae. The primary outcome is the incidence rate of microbiologically-positive viral ARI, using incidence rate ratios to estimate between-group differences. We hypothesize that among infants 0-6 months of age, the incidence of microbiologically-confirmed viral ARI will be significantly lower in infants whose mothers received high-dose prenatal/postpartum vitamin D supplements versus placebo. Secondary outcomes include incidence of ARI associated with specific pathogens (influenza A or B, RSV), clinical ARI, and density of pneumococcal carriage. DISCUSSION: If shown to reduce the risk of viral ARI in infancy, integration of maternal prenatal/postpartum vitamin D supplementation into antenatal care programs in South Asia may be a feasible primary preventive strategy to reduce the burden of ARI-associated morbidity and mortality in young infants. TRIAL REGISTRATION: NCT02388516 , registered March 9, 2015.


Subject(s)
Dietary Supplements , Infant, Newborn, Diseases/prevention & control , Lactation , Prenatal Care/methods , Respiratory Tract Infections/prevention & control , Vitamin D/administration & dosage , Vitamins/administration & dosage , Acute Disease , Adult , Bangladesh , Breast Feeding , Clinical Protocols , Female , Humans , Infant , Infant, Newborn , Infant, Newborn, Diseases/virology , Male , Maternal Nutritional Physiological Phenomena , Pregnancy , Prospective Studies , Respiratory Syncytial Virus Infections/prevention & control , Respiratory Syncytial Virus Infections/virology , Respiratory Tract Infections/virology , Treatment Outcome
15.
Curr Microbiol ; 68(5): 642-7, 2014 May.
Article in English | MEDLINE | ID: mdl-24452425

ABSTRACT

The environmental Escherichia albertii strain DM104, which cross-reacts serologically with Shigella dysenteriae was assessed for pathogenic properties, immunogenicity, and protective efficacy in different animal models to evaluate it as a vaccine candidate against S. dysenteriae, which causes the severe disease, shigellosis. The DM104 isolate was found to be non-invasive and did not produce any entero- or cyto-toxins. The strain also showed negative results in the mouse lethal activity assay. The non-pathogenic DM104 strain gave, however, a high protective efficacy as an ocularly administered vaccine in the guinea pig eye model against S. dysenteriae type 4 challenge. It also induced a high titer of serum IgG against S. dysenteriae type 4 whole cell lysate and lipopolysaccharide. Taken together, all these results indicate a good potential for the use of the DM104 as a live vaccine candidate against shigellosis.


Subject(s)
Bacterial Vaccines/immunology , Dysentery, Bacillary/prevention & control , Escherichia/immunology , Eye Diseases/prevention & control , Shigella dysenteriae/immunology , Vaccination/methods , Administration, Ophthalmic , Animals , Antibodies, Bacterial/blood , Bacterial Vaccines/administration & dosage , Dysentery, Bacillary/immunology , Environmental Microbiology , Escherichia/isolation & purification , Escherichia/pathogenicity , Eye Diseases/immunology , Guinea Pigs , Immunoglobulin G/blood , Mice
16.
One Health ; 18: 100681, 2024 Jun.
Article in English | MEDLINE | ID: mdl-39010948

ABSTRACT

Avian influenza virus (AIV) is of major concern to livestock, wildlife, and human health. In many countries in the world, including Bangladesh, AIV is endemic in poultry, requiring improving biosecurity. In Bangladesh, we investigated how variation in biosecurity practices in commercial chicken farms affected their AIV infection status to help guide AIV mitigation strategies. We collected pooled fecal swabs from 225 farms and tested the samples for the AIV matrix gene followed by H5, H7, and H9 subtyping using rRT-PCR. We found that 39.6% of chicken farms were AIV positive, with 13% and 14% being positive for subtypes H5 and H9, respectively. Using a generalized linear mixed effects model, we identified as many as 12 significant AIV risk factors. Two major factors promoting AIV risk that cannot be easily addressed in the short term were farm size and the proximity of the farm to a live bird market. However, the other ten significant determinants of AIV risk can be more readily addressed, of which the most important ones were limiting access by visitors (reducing predicted AIV risk from 42 to 6%), isolation and treatment of sick birds (42 to 7%), prohibiting access of vehicles to poultry sheds (38 to 8%), improving hand hygiene (from 42 to 9%), not sharing farm workers across farms (37 to 8%), and limiting access by wild birds to poultry sheds (37 to 8%). Our findings can be applied to developing practical and cost-effective measures that significantly decrease the prevalence of AIV in chicken farms. Notably, in settings with limited resources, such as Bangladesh, these measures can help governments strengthen biosecurity practices in their poultry industry to limit and possibly prevent the spread of AIV.

17.
Emerg Microbes Infect ; 13(1): 2399268, 2024 Dec.
Article in English | MEDLINE | ID: mdl-39207215

ABSTRACT

High pathogenicity avian influenza (HPAI) virus H5N1 first emerged in Bangladesh in 2007. Despite the use of vaccines in chickens since 2012 to control HPAI, HPAI H5Nx viruses have continued to infect poultry, and wild birds, resulting in notable mass mortalities in house crows (Corvus splendens). The first HPAI H5Nx viruses in Bangladesh belonged to clade 2.2.2, followed by clade 2.3.4.2 and 2.3.2.1 viruses in 2011. After the implementation of chicken vaccination in 2012, these viruses were mostly replaced by clade 2.3.2.1a viruses and more recently clade 2.3.4.4b and h viruses. In this study, we reconstruct the phylogenetic history of HPAI H5Nx viruses in Bangladesh to evaluate the role of major host species in the maintenance and evolution of HPAI H5Nx virus in Bangladesh and reveal the role of heavily impacted crows in virus epidemiology. Epizootic waves caused by HPAI H5N1 and H5N6 viruses amongst house crows occurred annually in winter. Bayesian phylodynamic analysis of clade 2.3.2.1a revealed frequent bidirectional viral transitions between domestic ducks, chickens, and house crows that was markedly skewed towards ducks; domestic ducks might be the source, or reservoir, of HPAI H5Nx in Bangladesh, as the number of viral transitions from ducks to chickens and house crows was by far more numerous than the other transitions. Our results suggest viral circulation in domestic birds despite vaccination, with crow epizootics acting as a sentinel. The vaccination strategy needs to be updated to use more effective vaccinations, assess vaccine efficacy, and extension of vaccination to domestic ducks, the key reservoir.


Subject(s)
Chickens , Disease Reservoirs , Ducks , Influenza in Birds , Phylogeny , Animals , Influenza in Birds/virology , Influenza in Birds/epidemiology , Influenza in Birds/prevention & control , Ducks/virology , Bangladesh/epidemiology , Disease Reservoirs/virology , Chickens/virology , Influenza A Virus, H5N1 Subtype/genetics , Influenza A Virus, H5N1 Subtype/pathogenicity , Influenza A Virus, H5N1 Subtype/immunology , Influenza A Virus, H5N1 Subtype/classification , Influenza A Virus, H5N1 Subtype/isolation & purification , Crows/virology , Animals, Wild/virology , Influenza A virus/genetics , Influenza A virus/pathogenicity , Influenza A virus/classification , Influenza A virus/immunology , Poultry Diseases/virology , Poultry Diseases/epidemiology , Poultry Diseases/prevention & control
18.
Microbiol Spectr ; 12(1): e0327223, 2024 Jan 11.
Article in English | MEDLINE | ID: mdl-38014980

ABSTRACT

IMPORTANCE: Affordable and accessible tests for COVID-19 allow for timely disease treatment and pandemic management. SalivaDirect is a faster and easier method to implement than NPS sampling. Patients can self-collect saliva samples at home or in other non-clinical settings without the help of a healthcare professional. Sample processing in SalivaDirect is less complex and more adaptable than in conventional nucleic acid extraction methods. We found that SalivaDirect has good diagnostic performance and is ideal for large-scale testing in settings where supplies may be limited or trained healthcare professionals are unavailable.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , Health Personnel , Pandemics , RNA , Saliva , Specimen Handling
19.
Emerg Microbes Infect ; 13(1): 2398640, 2024 Dec.
Article in English | MEDLINE | ID: mdl-39194145

ABSTRACT

Nipah virus (NiV) is an emerging zoonotic RNA virus that can cause fatal respiratory and neurological diseases in animals and humans. Accurate NiV diagnostics and surveillance tools are crucial for the identification of acute and resolved infections and to improve our understanding of NiV transmission and circulation. Here, we have developed and validated a split NanoLuc luciferase NiV glycoprotein (G) biosensor for detecting antibodies in clinical and animal samples. This assay is performed by simply mixing reagents and measuring luminescence, which depends on the complementation of the split NanoLuc luciferase G biosensor following its binding to antibodies. This anti-NiV-G "mix-and-read" assay was validated using the WHO's first international standard for anti-NiV antibodies and more than 700 serum samples from the NiV-endemic country of Bangladesh. Anti-NiV antibodies from survivors persisted for at least 8 years according to both ⍺NiV-G mix-and-read and NiV neutralization assays. The ⍺NiV-G mix-and-read assay sensitivity (98.6%) and specificity (100%) were comparable to anti-NiV IgG ELISA performance but failed to detect anti-NiV antibodies in samples collected less than a week following the appearance of symptoms. Overall, the anti-NiV-G biosensor represents a simple, fast, and reliable tool that could support the expansion of NiV surveillance and retrospective outbreak investigations.


Subject(s)
Antibodies, Viral , Biosensing Techniques , Henipavirus Infections , Nipah Virus , Nipah Virus/immunology , Antibodies, Viral/blood , Antibodies, Viral/immunology , Henipavirus Infections/diagnosis , Henipavirus Infections/immunology , Henipavirus Infections/virology , Humans , Biosensing Techniques/methods , Animals , Bangladesh/epidemiology , Luciferases/genetics , Sensitivity and Specificity , Female , Adult , Enzyme-Linked Immunosorbent Assay/methods , Male , Adolescent , Young Adult , Middle Aged
20.
Influenza Other Respir Viruses ; 18(7): e13352, 2024 Jul.
Article in English | MEDLINE | ID: mdl-39005150

ABSTRACT

BACKGROUND: Global influenza-associated acute respiratory infections contribute to 3-5 million severe illnesses requiring hospitalization annually, with 90% of hospitalizations occurring among children < 5 years in developing countries. In Bangladesh, the inadequate availability of nationally representative, robust estimates of influenza-associated hospitalizations limits allocation of resources for prevention and control measures. METHODS: This study used data from the hospital-based influenza surveillance (HBIS) system in Bangladesh from 2010 to 2019 and healthcare utilization surveys to determine hospital utilization patterns in the catchment area. We estimated annual influenza-associated hospitalization numbers and rates for all age groups in Bangladesh using WHO methods, adjusted for a 6-day-a-week enrollment schedule, selective testing of specimens from children under five, and healthcare-seeking behavior, based on the proportion of symptomatic community participants seeking healthcare within the past week. We then estimated national hospitalization rates by multiplying age-specific hospitalization rates with the corresponding annual national census population. RESULTS: Annual influenza-associated hospitalization rates per 100,000 population for all ages ranged from 31 (95% CI: 27-36) in 2011 to 139 (95% CI: 130-149) in 2019. Children < 5 years old had the highest rates of influenza-associated hospitalization, ranging from 114 (95% CI: 90-138) in 2011 to 529 (95% CI: 481-578) in 2019, followed by adults aged ≥ 65 years with rates ranging from 46 (95% CI: 34-57) in 2012 to 252 (95% CI: 213-292) in 2019. The national hospitalization estimates for all ages during 2010-2019 ranged from 47,891 to 236,380 per year. CONCLUSIONS: The impact of influenza-associated hospitalizations in Bangladesh may be considerable, particularly for young children and older adults. Targeted interventions, such as influenza vaccination for these age groups, should be prioritized and evaluated.


Subject(s)
Hospitalization , Influenza, Human , Humans , Bangladesh/epidemiology , Hospitalization/statistics & numerical data , Influenza, Human/epidemiology , Child, Preschool , Child , Infant , Adult , Incidence , Adolescent , Middle Aged , Young Adult , Aged , Female , Male , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Infant, Newborn , Aged, 80 and over , Acute Disease/epidemiology
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