Publications by authors named "Mustafizur Rahman"

170 Publications

Prevalence of COVID-19 in Bangladesh, April to October 2020-a cross-sectional study.

IJID Reg 2021 Dec 14;1:92-99. Epub 2021 Oct 14.

Directorate General of Health Services (DGHS), Dhaka, Bangladesh.

The aim of this study was to estimate the proportion of symptomatic and asymptomatic laboratory-confirmed coronavirus disease 2019 (COVID-19) cases among the population of Bangladesh. A cross-sectional survey was conducted in Dhaka City and other districts of Bangladesh between April 18 and October 12, 2020. A total of 32 districts outside Dhaka were randomly selected, and one village and one mahalla was selected from each district; 25 mahallas were selected from Dhaka City. From each village or mahalla, 120 households were enrolled through systematic random sampling. A total of 44 865 individuals were interviewed from 10 907 households. The majority (70%,  = 31 488) of the individuals were <40 years of age. Almost half of the individuals (49%,  = 21 888) reported more than four members in their household. It was estimated that 12.6% ( = 160) of the households had one or more severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected individuals, among whom 0.9% ( = 404) of individuals had at least one COVID-19-like symptom, at the national level. The prevalence of COVID-19 in the general population was 6.4%. Among the SARS-CoV-2-positive individuals, 87% were asymptomatic. The substantial high number of asymptomatic cases all over Bangladesh suggests that community-level containment and mitigation measures are required to combat COVID-19. Future studies to understand the transmission capability could help to define mitigation and control measures.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ijregi.2021.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8516147PMC
December 2021

Seroprevalence of SARS-CoV-2 antibodies in Bangladesh related to novel coronavirus infection.

IJID Reg 2022 Mar 2;2:198-203. Epub 2022 Feb 2.

International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh.

Design: A cross-sectional study was conducted amongst household members in 32 districts of Bangladesh to build knowledge about disease epidemiology and seroepidemiology of coronavirus disease 2019 (COVID-19).

Objective: Antibody responses to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) were assessed in people between April and October 2020.

Results: The national seroprevalence rates of immunoglobulin G (IgG) and IgM were estimated to be 30.4% and 39.7%, respectively. In Dhaka, the seroprevalence of IgG was 35.4% in non-slum areas and 63.5% in slum areas. In areas outside of Dhaka, the seroprevalence of IgG was 37.5% in urban areas and 28.7% in rural areas. Between April and October 2020, the highest seroprevalence rate (57% for IgG and 64% for IgM) was observed in August. IgM antibody was more prevalent in younger participants, while older participants had more frequent IgG seropositivity. Follow-up specimens from patients with COVID-19 and their household members suggested that both IgG and IgM seropositivity increased significantly at day 14 and day 28 compared with day 1 after enrolment. : SARS-CoV-2 had spread extensively in Bangladesh by October 2020. This highlights the importance of monitoring seroprevalence data, particularly with the emergence of new SARS-CoV-2 variants over time.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ijregi.2022.01.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8809641PMC
March 2022

COVID-19 among staff and their family members of a healthcare research institution in Bangladesh between March 2020 and April 2021: a test-negative case-control study.

BMJ Open 2022 06 1;12(6):e058074. Epub 2022 Jun 1.

Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh.

Objective: To identify factors associated with COVID-19 positivity among staff and their family members of icddr,b, a health research institute located in Bangladesh.

Setting: Dhaka, Bangladesh.

Participants: A total of 4295 symptomatic people were tested for SARS-CoV-2 by reverse-transcription PCR between 19 March 2020 and 15 April 2021. Multivariable logistic regression was done to identify the factors associated with COVID-19 positivity by contrasting test positives with test negatives.

Result: Forty-three per cent of the participants were tested positive for SARS-CoV-2. The median age was high in positive cases (37 years vs 34 years). Among the positive cases, 97% were recovered, 2.1% had reinfections, 24 died and 41 were active cases as of 15 April 2021. Multivariable regression analysis showed that age more than 60 years (adjusted OR (aOR)=2.1, 95% CI 1.3 to 3.3; p<0.05), blood group AB (aOR=1.5, 95% CI 1.1 to 2; p<0.05), fever (aOR=3.1, 95% CI 2.6 to 3.7; p<0.05), cough (aOR=1.3, 95% CI 1.1 to 1.6; p<0.05) and anosmia (aOR=2.7, 95% CI 1.3 to 5.7; p<0.05) were significantly associated with higher odds of being COVID-19 positive when compared with participants who were tested negative.

Conclusions: The study findings suggest that older age, fever, cough and anosmia were associated with COVID-19 among the study participants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/bmjopen-2021-058074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9160595PMC
June 2022

Transmission of SARS-CoV-2 in the Population Living in High- and Low-Density Gradient Areas in Dhaka, Bangladesh.

Trop Med Infect Dis 2022 Mar 25;7(4). Epub 2022 Mar 25.

Programme for Emerging Infections, Infectious Diseases Division, icddr,b, Dhaka 1212, Bangladesh.

Community transmission of SARS-CoV-2 in densely populated countries has been a topic of concern from the beginning of the pandemic. Evidence of community transmission of SARS-CoV-2 according to population density gradient and socio-economic status (SES) is limited. In June-September 2020, we conducted a descriptive longitudinal study to determine the community transmission of SARS-CoV-2 in high- and low-density areas in Dhaka city. The Secondary Attack Rate (SAR) was 10% in high-density areas compared to 20% in low-density areas. People with high SES had a significantly higher level of SARS-CoV-2-specific Immunoglobulin G (IgG) antibodies on study days 1 ( = 0.01) and 28 ( = 0.03) compared to those with low SES in high-density areas. In contrast, the levels of seropositivity of SARS-CoV-2-specific Immunoglobulin M (IgM) were comparable ( > 0.05) in people with high and low SES on both study days 1 and 28 in both high- and low-density areas. Due to the similar household size, no differences in the seropositivity rates depending on the population gradient were observed. However, people with high SES showed higher seroconversion rates compared to people with low SES. As no difference was observed based on population density, the SES might play a role in SARS-CoV-2 transmission, an issue that calls for further in-depth studies to better understand the community transmission of SARS-CoV-2.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/tropicalmed7040053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9030026PMC
March 2022

Prevalence of blindness and its determinants in Bangladeshi adult population: results from a national cross-sectional survey.

BMJ Open 2022 04 1;12(4):e052247. Epub 2022 Apr 1.

Research and Publication, World Health Organization, Dhaka, Bangladesh

Objective: The objective of this study was to determine the prevalence of blindness and its determinants in Bangladeshi adult population.

Study Design: A cross-sectional population-based survey conducted at household level with national representation. Samples were drawn from the 2011 national census frame using a multistage stratified cluster sampling method.

Setting And Participants: The survey was done in urban and rural areas in 2013 using a probability proportionate to size sampling approach to locate participants from 72 primary sampling units. One man or one woman aged ≥40 years was randomly selected from their households to recruit 7200. In addition to sociodemographic data, information on medication for hypertension and diabetes was obtained. Blood pressure and capillary blood glucose were measured. Eyelids, cornea, lens, and retina were examined in addition to visual acuity and refraction testing.

Primary Outcome Measures: The following definition was used to categorise subjects having (1) blindness: visual acuity <3/60, (2) low vision: ≥3/60 to <6/60 and (3) normal vision: ≥6/12 after best correction.

Results: We could recruit 6391 (88.8%) people among whom 2955 (46.2%) were men. Among them, 1922 (30.1%) were from urban and 4469 (69.9%) were from rural areas. The mean age was 54.3 (SD 11.2) years. The age-standardised prevalence, after best correction, of blindness and low vision was 1.0% (95% CI 0.5% to 1.4%) and 12.1% (95% CI 10.5% to 13.8%), respectively. Multivariable logistic regression indicated that cataract, age-related macular degeneration and diabetic retinopathy were significantly associated with low vision and blindness after adjustment for age and sex. Population attributable risk of cataract for low vision and blindness was 79.6%.

Conclusions: Low vision and blindness are common problems in those aged 40 years or older. Extensive screening and eye care services are necessary for wider coverage engaging all tiers of the healthcare system especially focusing on cataract.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/bmjopen-2021-052247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8977819PMC
April 2022

An adaptive synaptic array using Fowler-Nordheim dynamic analog memory.

Nat Commun 2022 03 29;13(1):1670. Epub 2022 Mar 29.

Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.

In this paper we present an adaptive synaptic array that can be used to improve the energy-efficiency of training machine learning (ML) systems. The synaptic array comprises of an ensemble of analog memory elements, each of which is a micro-scale dynamical system in its own right, storing information in its temporal state trajectory. The state trajectories are then modulated by a system level learning algorithm such that the ensemble trajectory is guided towards the optimal solution. We show that the extrinsic energy required for state trajectory modulation can be matched to the dynamics of neural network learning which leads to a significant reduction in energy-dissipated for memory updates during ML training. Thus, the proposed synapse array could have significant implications in addressing the energy-efficiency imbalance between the training and the inference phases observed in artificial intelligence (AI) systems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-022-29320-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8964701PMC
March 2022

Genome Sequences of 25 SARS-CoV-2 Sublineage B.1.1.529 Omicron Strains in Bangladesh.

Microbiol Resour Announc 2022 Apr 24;11(4):e0011922. Epub 2022 Mar 24.

Institute of Epidemiology, Disease Control, and Research, Dhaka, Bangladesh.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mra.00119-22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022525PMC
April 2022

Risk factors for bovine rotavirus infection and genotyping of bovine rotavirus in diarrheic calves in Bangladesh.

PLoS One 2022 25;17(2):e0264577. Epub 2022 Feb 25.

Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh.

Bovine rotavirus (BRV) is considered the leading cause of calf diarrhea worldwide, including Bangladesh. In this study we aimed to identify risk factors for BRV infection and determine the G and P genotypes of BRV strains in diarrheic calves. Fecal samples were collected from 200 diarrheic calves in three districts between January 2014 and October 2015. These samples were screened to detect the presence of BRV using rapid test-strips BIO K 152 (RTSBK). The RTSBK positive samples were further tested by polyacrylamide gel electrophoresis and the silver staining technique to detect rotavirus dsRNA. Risk factors were identified by multivariable logistic regression analysis. The G and P genotypes of BRV were determined by RT-PCR and sequencing. A phylogenetic tree was constructed based on the neighbor-joining method using CLC sequence viewer 8.0. About 23% of the diarrheic calves were BRV positive. The odds of BRV infection were 3.8- (95% confidence interval [95% CI]: 1.0-14.7) and 3.9-times (95% CI:1.1-14.2) higher in Barisal and Madaripur districts, respectively, than Sirrajganj. The risk of BRV infection was 3.1-times (95% CI: 1.5-6.5) higher in calves aged ≤ 5 weeks than those aged >5 weeks. Moreover, the risk of BRV infection was 2.6-times (95% CI:1.1-5.8) higher in crossbred (Holstein Friesian, Shahiwal) than indigenous calves. G6P[11] was the predominant genotype (94.4%), followed by G10P[11] (5.6%). The BRV G6 strains were found to be closest (98.9-99.9%) to Indian strains, and BRV G10 strains showed 99.9% identities with Indian strain. The VP4 gene of all P[11] strains showed >90% identities to each other and also with Indian strains. The most frequently identified BRV genotype was G6P[11]. About 23% of calf diarrhea cases were associated with BRV. To control disease, high-risk areas and younger crossbred calves should be targeted for surveillance and management. The predominant genotype could be utilized as the future vaccine candidate or vaccines with the dominant genotype should be used to control BRV diarrhea in Bangladesh.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0264577PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8880881PMC
March 2022

COVID-19 reinfections among naturally infected and vaccinated individuals.

Sci Rep 2022 01 26;12(1):1438. Epub 2022 Jan 26.

Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh.

The protection against emerging SARS-CoV-2 variants by pre-existing antibodies elicited due to the current vaccination or natural infection is a global concern. We aimed to investigate the rate of SARS-CoV-2 infection and its clinical features among infection-naïve, infected, vaccinated, and post-infection-vaccinated individuals. A cohort was designed among icddr,b staff registered for COVID-19 testing by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). Reinfection cases were confirmed by whole-genome sequencing. From 19 March 2020 to 31 March 2021, 1644 (mean age, 38.4 years and 57% male) participants were enrolled; where 1080 (65.7%) were tested negative and added to the negative cohort. The positive cohort included 750 positive patients (564 from baseline and 186 from negative cohort follow-up), of whom 27.6% were hospitalized and 2.5% died. Among hospitalized patients, 45.9% had severe to critical disease and 42.5% required oxygen support. Hypertension and diabetes mellitus were found significantly higher among the hospitalised patients compared to out-patients; risk ratio 1.3 and 1.6 respectively. The risk of infection among positive cohort was 80.2% lower than negative cohort (95% CI 72.6-85.7%; p < 0.001). Genome sequences showed that genetically distinct SARS-CoV-2 strains were responsible for reinfections. Naturally infected populations were less likely to be reinfected by SARS-CoV-2 than the infection-naïve and vaccinated individuals. Although, reinfected individuals did not suffer severe disease, a remarkable proportion of naturally infected or vaccinated individuals were (re)-infected by the emerging variants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-022-05325-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8792012PMC
January 2022

A Case Report: Genetically Distinct Severe Acute Respiratory Syndrome Coronavirus-2 Variant Causing Reinfection.

Front Microbiol 2021 9;12:792514. Epub 2021 Dec 9.

International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.

The emergence of novel variants has been a great deal of international concern since the recently published data suggest that previous infections with SARS-CoV-2 may not protect an individual from new variants. We report a patient had two distinct episodes of COVID-19 with different variants of SARS-CoV-2. The nasopharyngeal samples collected from the two episodes were subjected to whole-genome sequencing and comparative genome analysis. The first infection presented with mild symptoms, while the second infection presented with severe outcomes which occurred 74 days after the patient recovered from the first episode. He had elevated C-reactive protein, ferritin, and bilateral consolidation as a sign of acute infection. Genome analysis revealed that the strains from the first and second episodes belonged to two distinct Nexstrain clades 20B and 20I and Pangolin lineages B.1.1.25 and B.1.1.7, respectively. A total of 36 mutations were observed in the episode-2 strain when compared with the reference strain Wuhan-Hu-1. Among them, eight mutations were identified in the receptor-binding domain (RBD). Our findings concern whether the immunity acquired by natural infection or mass vaccination could confer adequate protection against the constantly evolving SARS-CoV-2. Therefore, continuous monitoring of genetic variations of SARS-CoV-2 strains is crucial for interventions such as vaccine and drug designs, treatment using monoclonal antibodies, and patient management.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2021.792514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8696118PMC
December 2021

Factors influencing the performance of rapid SARS-CoV-2 antigen tests under field condition.

J Clin Lab Anal 2022 Feb 23;36(2):e24203. Epub 2021 Dec 23.

Virology Laboratory, Infectious Diseases Division, icddr, b: International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jcla.24203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8842313PMC
February 2022

Establishing a sentinel surveillance system for the novel COVID-19 in a resource-limited country: methods, system attributes and early findings.

BMJ Open 2021 12 2;11(12):e055169. Epub 2021 Dec 2.

Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.

Objectives: To establish a hospital-based platform to explore the epidemiological and clinical characteristics of patients screened for COVID-19.

Design: Hospital-based surveillance.

Setting: This study was conducted in four selected hospitals in Bangladesh during 10 June-31 August 2020.

Participants: In total, 2345 patients of all age (68% male) attending the outpatient and inpatient departments of surveillance hospitals with any one or more of the following symptoms within last 7 days: fever, cough, sore throat and respiratory distress.

Outcome Measures: The outcome measures were COVID-19 positivity and mortality rate among enrolled patients. Pearson's χ test was used to compare the categorical variables (sign/symptoms, comorbidities, admission status and COVID-19 test results). Regression analysis was performed to determine the association between potential risk factors and death.

Results: COVID-19 was detected among 922 (39%) enrolled patients. It was more common in outpatients with a peak positivity in second week of July (112, 54%). The median age of the confirmed COVID-19 cases was 38 years (IQR: 30-50), 654 (71%) were male and 83 (9%) were healthcare workers. Cough (615, 67%) was the most common symptom, followed by fever (493, 53%). Patients with diabetes were more likely to get COVID-19 than patients without diabetes (48% vs 38%; OR: 1.5; 95% CI: 1.2 to 1.9). The death rate among COVID-19 positive was 2.3%, n=21. Death was associated with age ≥60 years (adjusted OR (AOR): 13.9; 95% CI: 5.5 to 34), shortness of breath (AOR: 9.7; 95% CI: 3.0 to 30), comorbidity (AOR: 4.8; 95% CI: 1.1 to 21.7), smoking history (AOR: 2.2, 95% CI: 0.7 to 7.1), attending the hospital in <2 days of symptom onset due to critical illness (AOR: 4.7; 95% CI: 1.2 to 17.8) and hospital admission (AOR: 3.4; 95% CI: 1.2 to 9.8).

Conclusions: COVID-19 positivity was observed in more than one-third of patients with suspected COVID-19 attending selected hospitals. While managing such patients, the risk factors identified for higher death rates should be considered.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/bmjopen-2021-055169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8640197PMC
December 2021

SARS-CoV-2 and influenza virus coinfection among patients with severe acute respiratory infection during the first wave of COVID-19 pandemic in Bangladesh: a hospital-based descriptive study.

BMJ Open 2021 11 29;11(11):e053768. Epub 2021 Nov 29.

Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.

Objective: To estimate the proportion of SARS-CoV-2 and influenza virus coinfection among severe acute respiratory infection (SARI) cases-patients during the first wave of COVID-19 pandemic in Bangladesh.

Design: Descriptive study.

Setting: Nine tertiary level hospitals across Bangladesh.

Participants: Patients admitted as SARI (defined as cases with subjective or measured fever of ≥38 C° and cough with onset within the last 10 days and requiring hospital admission) case-patients.

Primary And Secondary Outcomes: Proportion of SARS-CoV-2 and influenza virus coinfection and proportion of mortality among SARI case-patients.

Results: We enrolled 1986 SARI case-patients with a median age: 28 years (IQR: 1.2-53 years), and 67.6% were male. Among them, 285 (14.3%) were infected with SARS-CoV-2; 175 (8.8%) were infected with the influenza virus, and five (0.3%) were coinfected with both viruses. There was a non-appearance of influenza during the usual peak season (May to July) in Bangladesh. SARS-CoV-2 infection was significantly more associated with diabetes (14.0% vs 5.9%, p<0.001) and hypertension (26.7% vs 11.5%, p<0.001). But influenza among SARI case-patients was significantly less associated with diabetes (4.0% vs 7.4%, p=0.047) and hypertension (5.7% vs 14.4%, p=0.001). The proportion of in-hospital deaths among SARS-CoV-2 infected SARI case-patients were higher (10.9% (n=31) vs 4.4% (n=75), p<0.001) than those without SARS-CoV-2 infection; the proportion of postdischarge deaths within 30 days was also higher (9.1% (n=25) vs 4.6% (n=74), p=0.001) among SARS-CoV-2 infected SARI case-patients than those without infection. No in-hospital mortality or postdischarge mortality was registered among the five coinfected SARI case-patients.

Conclusions: Our findings suggest that coinfection with SARS-CoV-2 and influenza virus was not very common and had less disease severity considering mortality in Bangladesh. There was no circulating influenza virus during the influenza peak season during the COVID-19 pandemic in 2020. Future studies are warranted for further exploration.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/bmjopen-2021-053768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8634662PMC
November 2021

Clinical evaluation of SARS-CoV-2 antigen-based rapid diagnostic test kit for detection of COVID-19 cases in Bangladesh.

Heliyon 2021 Nov 22;7(11):e08455. Epub 2021 Nov 22.

Infectious Diseases Division (IDD), icddr,b, 68, Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh.

The rapid and early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is key to control the current Coronavirus disease 2019 (COVID-19) pandemic. The present study was conducted to clinically evaluate a rapid diagnostic test (RDT) kit, Standard Q COVID-19 Ag Test (SD Biosensor®, Republic of Korea), with reference to the standard real-time RT-PCR for detection of COVID-19 cases in Bangladesh. Nasopharyngeal swabs were taken from 900 COVID-19 suspected patients. Among them, 34.11% (n = 307) were diagnosed as COVID-19 cases by RT-PCR assay, of which 85% (n = 261) were also detectable using the RDT. The overall sensitivity and specificity of the RDT compared to RT-PCR were 85.02% and 100%, respectively, regardless of age, sex, and type of SARS-CoV-2 variants. Most of the RT-PCR positive cases (94%) were found within the first five days of disease onset, and the sensitivity of RDT was 85.91% for the same samples. The positive predictive value (PPV) of the RDT was 100%, and the negative predictive value (NPV) was 92.8%. The Cohen's kappa value of 0.882 indicated excellent agreement between the RDT and RT-PCR assays. The findings of this study showed the potential use of SARS-CoV-2 antigen-based RDT to expedite the diagnostic process and onward COVID-19 management in Bangladesh.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.heliyon.2021.e08455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606316PMC
November 2021

Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings.

Int J Infect Dis 2022 Jan 7;114:105-111. Epub 2021 Nov 7.

Emerging Infections and Parasitology Laboratory, NCSD, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, 1212, Bangladesh; Laboratory Science and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, 1212, Bangladesh. Electronic address:

Objectives: The democratization of diagnostics is one of the key challenges towards containing the transmission of coronavirus disease 2019 (COVID-19) around the globe. The operational complexities of existing PCR-based methods, including sample transfer to advanced central laboratories with expensive equipment, limit their use in resource-limited settings. However, with the advent of isothermal technologies, the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is possible at decentralized facilities.

Methods: In this study, two recombinase-based isothermal techniques, reverse transcription recombinase polymerase amplification (RT-RPA) and reverse transcription recombinase-aided amplification (RT-RAA), were evaluated for the detection of SARS-CoV-2 in clinical samples. A total of 76 real-time reverse transcription PCR (real-time RT-PCR) confirmed COVID-19 cases and 100 negative controls were evaluated to determine the diagnostic performance of the isothermal methods.

Results: This investigation revealed equally promising diagnostic accuracy of the two methods, with a sensitivity of 76.32% (95% confidence interval 65.18-85.32%) when the target genes were RdRP and ORF1ab for RT-RPA and RT-RAA, respectively; the combination of N and RdRP in RT-RPA augmented the accuracy of the assay at a sensitivity of 85.53% (95% confidence interval 75.58-92.55%). Furthermore, high specificity was observed for each of the methods, ranging from 94.00% to 98.00% (95% confidence interval 87.40-9.76%).

Conclusions: Considering the diagnostic accuracies, both RT-RPA and RT-RAA appear to be suitable assays for point-of-need deployment for the detection of the pathogen, understanding its epidemiology, case management, and curbing transmission.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ijid.2021.11.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8572376PMC
January 2022

Diagnostic Performance of Self-Collected Saliva Versus Nasopharyngeal Swab for the Molecular Detection of SARS-CoV-2 in the Clinical Setting.

Microbiol Spectr 2021 12 3;9(3):e0046821. Epub 2021 Nov 3.

Infectious Diseases Division, icddr,b, Dhaka, Bangladesh.

Coronavirus disease 19 (COVID-19)-caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-has spread rapidly around the world. The global shortage of equipment and health care professionals, diagnostic cost, and difficulty in collecting nasopharyngeal swabs (NPSs) necessitate the use of an alternative specimen type for SARS-CoV-2 diagnosis. In this study, we investigated the use of saliva as an alternative specimen type for SARS-CoV-2 detection. Participants presenting COVID-19 symptoms and their contacts were enrolled at the COVID-19 Screening Unit of Dhaka Hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), from July to November 2020. Paired NPS and saliva specimens were collected from each participant. Reverse transcription-quantitative PCR (RT-qPCR) was performed to detect SARS-CoV-2. Of the 596 suspected COVID-19-positive participants, 231 (38.7%) were detected as COVID-19 positive by RT-qPCR from at least 1 specimen type. Among the positive cases, 184 (79.6%) patients were identified to be positive for SARS-CoV-2 based on NPS and saliva samples, whereas 45 (19.65%) patients were positive for SARS-CoV-2 based on NPS samples but negative for SARS-CoV-2 based on the saliva samples. Two (0.5%) patients were positive for SARS-CoV-2 based on saliva samples but negative for SARS-CoV-2 based on NPS samples. The sensitivity and specificity of the saliva samples were 80.3% and 99.4%, respectively. SARS-CoV-2 detection was higher in saliva (85.1%) among the patients who visited the clinic after 1 to 5 days of symptom onset. A lower median cycle threshold () value indicated a higher SARS-CoV-2 viral load in NPS than that in saliva for target genes among the positive specimens. The study findings suggest that saliva can be used accurately for diagnosis of SARS-CoV-2 early after symptom onset in clinical and community settings. As the COVID-19 pandemic erupted, the WHO recommended the use of nasopharyngeal or throat swabs for the detection of SARS-CoV-2 etiology of COVID-19. The collection of NPS causes discomfort because of its invasive collection procedure. There are considerable risks to health care workers during the collection of these specimens. Therefore, an alternative, noninvasive, reliable, and self-collected specimen was explored in this study. This study investigated the feasibility and suitability of saliva versus NPS for the detection of SARS-CoV-2. Here, we showed that the sensitivity of saliva specimens was 80.35%, which meets the WHO criteria. Saliva is an easy-to-get, convenient, and low-cost specimen that yields better results if it is collected within the first 5 days of symptom onset. Our study findings suggest that saliva can be used in low-resource countries, community settings, and vulnerable groups, such as children and elderly people.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/Spectrum.00468-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8567243PMC
December 2021

Genome Sequences of SARS-CoV-2 Sublineage B.1.617.2 Strains from 12 Children in Chattogram, Bangladesh.

Microbiol Resour Announc 2021 Oct 21;10(42):e0091221. Epub 2021 Oct 21.

Virology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.

We announce the complete genome sequences of 12 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineage B.1.617.2 strains (Delta variant) obtained from nasopharyngeal and oropharyngeal swab samples from 12 pediatric patients in Chittagong, Bangladesh, displaying COVID-19 symptoms. Oxford Nanopore MinION sequencing technology was used to generate the genomic sequences.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/MRA.00912-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8530031PMC
October 2021

Drug resistance pattern among ART-naive clients attending an HIV testing and counseling center in Dhaka, Bangladesh.

J Med Virol 2022 02 16;94(2):787-790. Epub 2021 Oct 16.

Virology Laboratory, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.

In Bangladesh, antiretroviral therapy (ART) is provided without screening drug resistance-associated mutations (DRM) among people living with HIV, while DRM might emerge and transmit to the newly infected individual. The present study was aimed to identify DRM among ART-naive clients from an HIV testing and counseling (HTC) center in the initial stages of ART programs. Randomly selected (n = 64) archived plasma samples were used for the pol gene amplification and sequencing by sanger technology. Recovered sequences (n = 10) were genotyped using HIV genotyping tools of NCBI and analyzed using the Stanford University HIV drug resistance database (hivdb.stanford.edu). Various genotypes with a number of DRM were identified in HTC clients, who belonged to different risk groups based on behavioral data. The drug resistance algorithm showed that all samples were fully resistant to tipranavir/ritonavir drugs except for one intermediate resistance. Despite the small sample size, our understanding from this study warrants an ART policy with a DRM monitoring system for the country.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jmv.27387DOI Listing
February 2022

Influence of environmental factors on biology and catch composition of Barbonymus schwanenfeldii in a tropical lake, northern Malaysia: implications for conservation planning.

Environ Sci Pollut Res Int 2022 Feb 30;29(9):13661-13674. Epub 2021 Sep 30.

Department of Biotechnology, Faculty of Science, IIUM, Jalan Sultan Ahmad Shah, 25200, Kuantan, Pahang, Malaysia.

Very little work has determined the relative importance of uncontrolled environmental factors for affecting fish biology, and how these might influence gillnet catches. This study addresses this deficit for an important Southeast Asian cyprinid (Barbonymus schwanenfeldii). Fish were caught monthly for 12 months using gillnets of three different mesh sizes, each of which was deployed in duplicate at the surface of one of three randomly selected sites in Lake Kenyir, Malaysia, concurrent with determining various environmental parameters and the abundance of phytoplankton (chlorophyll-a). Results indicated that growth co-efficient of B. schwanenfeldii was positively influenced by dissolved oxygen and negatively influenced by total inorganic nitrogen, whereas an opposite result was observed in case of the hepatosomatic index of fish. Water turbidity was a limiting factor only for small fish (mean total length: 15.74±1.10 cm). B. schwanenfeldii could best be caught during the period of high phytoplankton abundance or at the location of high phytoplankton density in the water. Water temperature negatively influenced the gillnet catches of the fish. The remaining environmental factors such as water depth, pH, and phosphate had a weak and insignificant influence (P >0.05) on the biology and gillnet catches of fish. The observed results can be very useful for the ecological monitoring and conservation plans for this species in relation to climate change. Furthermore, the utility of the similar data for other species would be useful not only for regional but also for international fishery by optimizing catches considering environmental conditions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11356-021-16502-wDOI Listing
February 2022

Viral Etiology of Acute Gastroenteritis Among Forcibly Displaced Myanmar Nationals and Adjacent Host Population in Bangladesh.

J Infect Dis 2021 12;224(12 Suppl 2):S864-S872

International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/infdis/jiab466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8687051PMC
December 2021

Coding-Complete Sequence of a SARS-CoV-2 B.1.1.25 Lineage Obtained from an 8-Day-Old Deceased Neonate.

Microbiol Resour Announc 2021 Sep 2;10(35):e0075621. Epub 2021 Sep 2.

Virology Laboratory, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh.

We report the complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain, hCoV-19/Bangladesh/icddrb-CHAMPS-BDAA02205/2021, obtained from a nasopharyngeal swab from a deceased neonate from Faridpur, Bangladesh. The strain belongs to lineage B.1.1.25 but contains some notable mutations similar to the B.1.1.7 lineage.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/MRA.00756-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8411918PMC
September 2021

Deaths Attributed to Respiratory Syncytial Virus in Young Children in High-Mortality Rate Settings: Report from Child Health and Mortality Prevention Surveillance (CHAMPS).

Clin Infect Dis 2021 09;73(Suppl_3):S218-S228

Instituto Nacional de Saúde, Maputo, Mozambique.

Background: Lower respiratory tract infections are a leading cause of death in young children, but few studies have collected the specimens needed to define the role of specific causes. The Child Health and Mortality Prevention Surveillance (CHAMPS) platform aims to investigate causes of death in children aged <5 years in high-mortality rate settings, using postmortem minimally invasive tissue sampling and other advanced diagnostic techniques. We examined findings for deaths identified in CHAMPS sites in 7 countries in sub-Saharan Africa and south Asia to evaluate the role of respiratory syncytial virus (RSV).

Methods: We included deaths that occurred between December 2016 and December 2019. Panels determined causes of deaths by reviewing all available data including pathological results from minimally invasive tissue sampling, polymerase chain reaction screening for multiple infectious pathogens in lung tissue, nasopharyngeal swab, blood, and cerebrospinal fluid samples, clinical information from medical records, and verbal autopsies.

Results: We evaluated 1213 deaths, including 695 in neonates (aged <28 days), 283 in infants (28 days to <12 months), and 235 in children (12-59 months). RSV was detected in postmortem specimens in 67 of 1213 deaths (5.5%); in 24 deaths (2.0% of total), RSV was determined to be a cause of death, and it contributed to 5 other deaths. Younger infants (28 days to <6 months of age) accounted for half of all deaths attributed to RSV; 6.5% of all deaths in younger infants were attributed to RSV. RSV was the underlying and only cause in 4 deaths; the remainder (n = 20) had a median of 2 (range, 1-5) other conditions in the causal chain. Birth defects (n = 8) and infections with other pathogens (n = 17) were common comorbid conditions.

Conclusions: RSV is an important cause of child deaths, particularly in young infants. These findings add to the substantial body of literature calling for better treatment and prevention options for RSV in high-mortality rate settings.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/cid/ciab509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8411256PMC
September 2021

The Etiology of Childhood Pneumonia in Bangladesh: Findings From the Pneumonia Etiology Research for Child Health (PERCH) Study.

Pediatr Infect Dis J 2021 09;40(9S):S79-S90

From the Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.

Background: Pneumonia remains the leading infectious cause of death among children <5 years, but its cause in most children is unknown. We estimated etiology for each child in 2 Bangladesh sites that represent rural and urban South Asian settings with moderate child mortality.

Methods: As part of the Pneumonia Etiology Research for Child Health study, we enrolled children 1-59 months of age with World Health Organization-defined severe and very severe pneumonia, plus age-frequency-matched controls, in Matlab and Dhaka, Bangladesh. We applied microbiologic methods to nasopharyngeal/oropharyngeal swabs, blood, induced sputum, gastric and lung aspirates. Etiology was estimated using Bayesian methods that integrated case and control data and accounted for imperfect sensitivity and specificity of the measurements.

Results: We enrolled 525 cases and 772 controls over 24 months. Of the cases, 9.1% had very severe pneumonia and 42.0% (N = 219) had infiltrates on chest radiograph. Three cases (1.5%) had positive blood cultures (2 Salmonella typhi, 1 Escherichia coli and Klebsiella pneumoniae). All 4 lung aspirates were negative. The etiology among chest radiograph-positive cases was predominantly viral [77.7%, 95% credible interval (CrI): 65.3-88.6], primarily respiratory syncytial virus (31.2%, 95% CrI: 24.7-39.3). Influenza virus had very low estimated etiology (0.6%, 95% CrI: 0.0-2.3). Mycobacterium tuberculosis (3.6%, 95% CrI: 0.5-11.0), Enterobacteriaceae (3.0%, 95% CrI: 0.5-10.0) and Streptococcus pneumoniae (1.8%, 95% CrI: 0.0-5.9) were the only nonviral pathogens in the top 10 etiologies.

Conclusions: Childhood severe and very severe pneumonia in young children in Bangladesh is predominantly viral, notably respiratory syncytial virus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/INF.0000000000002648DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8448409PMC
September 2021

Epidemiology of the Rhinovirus (RV) in African and Southeast Asian Children: A Case-Control Pneumonia Etiology Study.

Viruses 2021 06 27;13(7). Epub 2021 Jun 27.

Department of Paediatrics and Child Health, University Teaching Hospital, Lusaka 50110, Zambia.

Rhinovirus (RV) is commonly detected in asymptomatic children; hence, its pathogenicity during childhood pneumonia remains controversial. We evaluated RV epidemiology in HIV-uninfected children hospitalized with clinical pneumonia and among community controls. PERCH was a case-control study that enrolled children (1-59 months) hospitalized with severe and very severe pneumonia per World Health Organization clinical criteria and age-frequency-matched community controls in seven countries. Nasopharyngeal/oropharyngeal swabs were collected for all participants, combined, and tested for RV and 18 other respiratory viruses using the Fast Track multiplex real-time PCR assay. RV detection was more common among cases (24%) than controls (21%) (aOR = 1.5, 95%CI:1.3-1.6). This association was driven by the children aged 12-59 months, where 28% of cases vs. 18% of controls were RV-positive (aOR = 2.1, 95%CI:1.8-2.5). Wheezing was 1.8-fold (aOR 95%CI:1.4-2.2) more prevalent among pneumonia cases who were RV-positive vs. RV-negative. Of the RV-positive cases, 13% had a higher probability (>75%) that RV was the cause of their pneumonia based on the PERCH integrated etiology analysis; 99% of these cases occurred in children over 12 months in Bangladesh. RV was commonly identified in both cases and controls and was significantly associated with severe pneumonia status among children over 12 months of age, particularly those in Bangladesh. RV-positive pneumonia was associated with wheezing.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/v13071249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8310211PMC
June 2021

The emergence of SARS-CoV-2 variants in Dhaka city, Bangladesh.

Transbound Emerg Dis 2021 11 2;68(6):3000-3001. Epub 2021 Jul 2.

Virology Laboratory, icddr,b: International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tbed.14203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8447378PMC
November 2021

Epidemiology and genetic characterization of human sapovirus among hospitalized acute diarrhea patients in Bangladesh, 2012-2015.

J Med Virol 2021 11 10;93(11):6220-6228. Epub 2021 Jun 10.

Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh.

Human sapovirus, which causes acute gastroenteritis, is not well studied and poorly understood. This study aims to investigate the contribution of sapovirus in diarrhea, their clinical association, and genotypic diversity. Fecal specimens (n = 871) were randomly selected from diarrheal patients who attended International Centre for Diarrhoeal Disease Research, Bangladesh hospital in Dhaka, Bangladesh during January 2012-December 2015 and tested for the presence of sapovirus RNA using real-time polymerase chain reaction. Sapovirus RNA was identified in 2.3% (n = 20) of the samples. Seventy-five percent of the sapovirus positive cases were coinfected with other pathogens, such as rotavirus, norovirus, enterotoxigenic Escherichia coli, adenovirus, Shigella spp., and Vibrio cholerae. A vast genetic diversity was observed among sapovirus with at least seven common genotypes (GI.1, GI.2, GI.7, GII.1, GII.4, GII.6, and GIV), and a new genotype GII.NA1. Some of the GI.1 strains detected were similar to GI.4 in the polymerase region sequence and were confirmed as recombinant strains. Our findings suggest that the overall contribution of sapovirus in hospitalized diarrheal illness is low but highlight enormous genetic diversity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jmv.27125DOI Listing
November 2021

Genome Sequencing Identified a SARS-CoV-2 Lineage B.1.1.7 Strain with a High Number of Mutations from Dhaka, Bangladesh.

Microbiol Resour Announc 2021 May 27;10(21):e0034521. Epub 2021 May 27.

Genomics Center, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.

We report a coding-complete genome sequence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain SARS-CoV-2/BGD/GC001, isolated from a Bangladeshi patient with respiratory symptoms. Phylogenetic analysis assigned this strain to lineage B.1.1.7, which presented a total of 36 mutations in the spike and other genomic regions compared to strain Wuhan Hu-1 (GenBank accession number NC_045512.2).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/MRA.00345-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8201627PMC
May 2021

Upper Respiratory Tract Co-detection of Human Endemic Coronaviruses and High-density Pneumococcus Associated With Increased Severity Among HIV-Uninfected Children Under 5 Years Old in the PERCH Study.

Pediatr Infect Dis J 2021 06;40(6):503-512

Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland.

Background: Severity of viral respiratory illnesses can be increased with bacterial coinfection and can vary by sex, but influence of coinfection and sex on human endemic coronavirus (CoV) species, which generally cause mild to moderate respiratory illness, is unknown. We evaluated CoV and pneumococcal co-detection by sex in childhood pneumonia.

Methods: In the 2011-2014 Pneumonia Etiology Research for Child Health study, nasopharyngeal and oropharyngeal (NP/OP) swabs and other samples were collected from 3981 children <5 years hospitalized with severe or very severe pneumonia in 7 countries. Severity by NP/OP detection status of CoV (NL63, 229E, OC43 or HKU1) and high-density (≥6.9 log10 copies/mL) pneumococcus (HDSpn) by real-time polymerase chain reaction was assessed by sex using logistic regression adjusted for age and site.

Results: There were 43 (1.1%) CoV+/HDSpn+, 247 CoV+/HDSpn-, 449 CoV-/HDSpn+ and 3149 CoV-/HDSpn- cases with no significant difference in co-detection frequency by sex (range 51.2%-64.0% male, P = 0.06). More CoV+/HDSpn+ pneumonia was very severe compared with other groups for both males (13/22, 59.1% versus range 29.1%-34.7%, P = 0.04) and females (10/21, 47.6% versus 32.5%-43.5%, P = 0.009), but only male CoV+/HDSpn+ required supplemental oxygen more frequently (45.0% versus 20.6%-28.6%, P < 0.001) and had higher mortality (35.0% versus 5.3%-7.1%, P = 0.004) than other groups. For females with CoV+/HDSpn+, supplemental oxygen was 25.0% versus 24.8%-33.3% (P = 0.58) and mortality was 10.0% versus 9.2%-12.9% (P = 0.69).

Conclusions: Co-detection of endemic CoV and HDSpn was rare in children hospitalized with pneumonia, but associated with higher severity and mortality in males. Findings may warrant investigation of differences in severity by sex with co-detection of HDSpn and SARS-CoV-2.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/INF.0000000000003139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8104011PMC
June 2021
-->