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Background: COVID-19 has now become a pandemic. Objective: The aim of this study was to characterize the demographic features with infection rate of SARS-CoV-2 in 4/5 divisions of Bangladesh. Methodology: This cross-sectional study was conducted at National institute of Laboratory Medicine and Referral Center, Dhaka, Bangladesh from 15th April to 30th April, 2020. It was performed RT-PCR for 2462 cases within the time frame and 1082 samples were positive for SARS CoV-2. Patient demographic characteristics including age, gender, occupation and blood group was investigated. Results: The mean age of positive cases was 40.2 ± 15.33 years, 426 (39%) cases were 25-39 years of age. The majority of cases were male (71%) and the predominant blood group was B positive (37%). Conclusions: In conclusion male gender, younger age and blood group B positive are more commonly suffering from COVID-19 infection. Bangladesh Journal of Infectious Diseases, October 2020;7(suppl_2):S22-S26

Background: Increased antimicrobial consumption has increased the burden on worsening situation of antimicrobial resistance throughout the world. Objective: The purpose of this study was to assess the practice of irrational antibiotic prescribing and consumption among COVID-19 positive patients of Bangladesh and its possible impact on existing AMR. Methodology: This was a cross-sectional study conducted among SARS-CoV-2 positive patients from a tertiary COVID-19 PCR testing center in Dhaka between 10th July 2020 and 20th July 2020. A validated questionnaire was used to gather data. Ethical approval was obtained. A total of 100 participants through random sampling was selected. Results: A total of 100 COVID-19 RT-PCR positive patients were participated in this study: 96% had mild symptoms, fever (81.0%) was the most common presenting symptoms, 45.0% patients did not consult with physicians even after knowing their positive test results and reported self medicating with antibiotics, and 36.0% were treated with multiple antibiotics and antiviral at a time. Azithromycin (46.0%), Ivermectin (22.0%) and doxycycline (21.0%) were the antibiotics most used, which were mainly obtained from local retail pharmacies. Conclusion: Practice of irrational antibiotic prescribing and self medication is relatively high among COVID-19 positive participants. Bangladesh Journal of Infectious Diseases, October 2020;7(suppl_2):S3-S7

With the COVID-19 pandemic, disparities between the infection rate and death rate in different countries become a major concern. In some countries, lower mortality rate compared to others can be explained by better testing capacity and intensive care facilities. Complete SARS-CoV-2 genome sequences from different countries of the world are continually submitted to Global Initiative for Sharing All Influenza Data using Next Generation Sequencing method. A SARS-CoV-2 variant with a D 614G Mutation in the spike (S) protein has become the most dominant form in the global pandemic. There are a number of ongoing studies trying to relate this mutation with the infectivity, mortality, transmissibility of the virus and its impact on vaccine development. This review aims to accumulate the major findings from some of these studies and focus its future implication. Some studies suggested D 614G strain has increased binding capacity, it affects more cells at a faster rate, so has a high transmissibility. Patients infected with this strain were found with high viral load. But still now there is no such evidence that this strain produces more severe disease as well as increased mortality. The structural change of spike protein produced by D 614G mutation was minor and did not hamper the vaccine efficacy. Some studies showed antibodies produced against D614 strain can neutralize G614 strain and vice versa. Whenever a mutation occurs in spike protein there are always chances of affecting the infectivity, transmissibility, vaccine efficacy. Therefore, more studies are required to find out the overall effect of D 614G mutation.

We report the near-complete genome sequence and phylogenetic analysis of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) strain. This variant is associated with increased transmission and immune evasion.

Novel SARS-CoV-2 variants are emerging at an alarming rate. The delta variant and other variants of concern (VoC) carry spike (S)-protein mutations, which have the potential to evade protective immunity, to trigger break-through infections after COVID-19 vaccination, and to propagate future waves of COVID-19 pandemic. To identify SARS CoV-2 variants in Bangladesh, patients who are RT-PCR-positive for COVID-19 infections in Dhaka were screened by a RT-PCR melting curve analysis for spike protein mutations. To assess the anti-SARS CoV-2 antibody responses, the levels of the anti-S -proteins IgA and IgG and the anti-N-protein IgG were measured by ELISA. Of a total of 36 RT-PCR positive samples (75%), 27 were identified as delta variants, with one carrying an additional Q677H mutation and two with single nucleotide substitutions at position 23029 (compared to Wuhan-Hu-1 reference NC 045512) in the genome sequence. Three (8.3%) were identified as beta variants, two (5.5%) were identified as alpha variants, three (8.3%) were identified as having a B.1.1.318 lineage, and one sample was identified as an eta variant (B.1.525) carrying an additional V687L mutation. The trend of higher viral load (lower Cp values) among delta variants than in the alpha and beta variants was of borderline statistical significance (p = 0.045). Prospective studies with larger Bangladeshi cohorts are warranted to confirm the emergence of S-protein mutations and their association with antibody response in natural infection and potential breakthrough in vaccinated subjects.

To better comprehend the genetic epidemiology of SARS-CoV-2, we utilized NextSeq 550 to conduct whole-genome sequencing of certain samples in Bangladesh. The samples were taken from the nasopharyngeal swabs of 17 persons who had tested positive for COVID-19 using RT-PCR. Following the sequencing, the data was uploaded to the GISAID database and evaluated by comparing their nucleotide alterations to the Wuhan SARS-CoV-2 reference genome. Based on phylogenetic and mutation studies, it was shown that 88% belong to the pangolin lineage B.1.1.25, whereas 11% corresponds to its parent lineage B.1.1. We also compared the spike protein sequences of two isolates (BCSIR-NILMRC-422 and BCSIR-NILMRC-424) to the reference genome and observed two mutations including, D614G and P681R, at positions 614 and 681, respectively. Although D614G being the most frequent, not present in every isolate. Using standard mode studies, we also looked at molecular dynamics and discovered that this SNP reduces the S1 domain's flexibility. This finding suggests that the P681R mutation is a distinguishing feature of this novel voice of concern’s virological profile, which may be linked to viral pathogenicity in Bangladeshi patients.

Background and Aims It is postulated that molecular methods along with mathematical modeling can provide critical inference regarding epidemiological parameters, transmission dynamics, spatiotemporal characteristics, and intervention efficacy. Hence, studying molecular epidemiology of human immunodeficiency virus (HIV)‐1 infection, especially in resource‐limited settings and with a large diaspora of the migrant population such as that of Bangladesh, is of paramount importance. The purpose of this systematic review was to concisely present and discuss the findings from previous studies conducted in Bangladesh regarding HIV‐1 subtype prevalence. Methods Articles were retrieved from six publicly available databases regarding HIV‐1 molecular epidemiology using keywords HIV, HIV‐1, subtype(s), Bangladesh, and any combination of aforementioned keywords using Boolean operators. A total of 14 articles were downloaded and screened for suitability. Finally, five studies, containing pooled sequences from 317 individuals, were included in this systematic review. Results Results revealed a preponderance of subtype C among HIV‐1 infected population (51.10%), followed by circulating recombinant form (CRF)_07BC (15.46%), CRF_01AE (5.68%), A1 (4.73%), CRF_02AG (3.47%), G (3.15%), CRF_62BC (2.84%), B (2.21%), and other subtypes and recombinant forms in small percentages. Subtype C was largely predominant in intravenous drug users as well as female sex workers, whereas the migrant population exhibited a diverse subtype including rare recombinant forms, largely due to their travel in the Middle East and other South East Asian countries. Conclusion With the number of HIV‐1 infections increasing among the general population and a steady increase in the migrant population, molecular epidemiological data are required to curb the progression of the HIV‐1 epidemic in Bangladesh.

Background: The World Health Organization (WHO) declared COVID-19 as a pandemic on the 11th of March 2020. Since then, many efforts are being carried out to contain the virus. Knowledge and attitude of people should be directed towards strict preventive practices in order to halt the spread of the virus. The aim of the current cross-sectional study is to assess the knowledge, practice and attitude of healthcare workers (HCWs) of National Institute of Laboratory Medicine and Referral Centre, Dhaka, Bangladesh using a structured questionnaire. Methods: A cross-sectional study among 139 healthcare persons was performed between April 2020 and May 2020 at National Institute of Laboratory Medicine and Referral Centre. A systematic random sampling strategy was carried out and the data was collected through a self-administered questionnaire of the knowledge, attitude and practice of healthcare workers regarding COVID-19. Results: About 87.2% of eligible subjects completed and returned the questionnaire had a mean age of (30.1±6.1) years, most of them were male (75.53%), the highest percentage of HCWs were medical technologists (53.23%) and the majority of them had less than 5 years’ experience (45.3%). A total of 96.4 % of the respondents were aware of coughing and sneezing etiquette, 93.52% followed hand washing steps but only 70% knew the duration of the hand hygiene procedure, while 89.92% uses face mask when go outside. The main sources of COVID-19 information were social media and the CDC/WHO website (38% and 23%, respectively). Conclusions: The majority of HCWs had good knowledge and positive attitude toward COVID-19. However, the level of some knowledge and attitude lower than that expected for their position level towards the virus. So, there is a need for awareness campaigns to improve their knowledge, in some aspects.

Summary Background As evidence is mounting regarding irrational and often unnecessary use of antibiotics during the COVID-19 pandemic a cross-sectional Point Prevalence Survey (PPS) (in accordance with WHO guideline) was conducted across COVID-19 dedicated wards in Dhaka Medical College and Hospital (DMCH). Methodology Antibiotic usage data were collected from 193 patients at different COVID-19 dedicated wards at DMCH on 11 June 2020. Comparisons in antibiotic usage were made between different groups using Pearson chi-square and Fisher's exact test. Result Findings reveal all surveyed patients (100%) were receiving at least one antibiotic with 133 patients (68.91%) receiving multiple antibiotics. Overall, patients presenting with the severe disease received more antibiotics. Third-generation cephalosporins (i.e. ceftriaxone) (53.8%), meropenem (40.9%), moxifloxacin (29.5%), and doxycycline (25.4%) were the four most prescribed antibiotics among surveyed patients. Diabetes mellitus (DM) was independently associated with multiple antibiotic prescribing. Abnormal C-reactive protein (CRP) and serum d-dimer were linked with higher odds of multiple antibiotic prescribing among study patients. Conclusion Prevalence of multiple antibiotic prescriptions was high among severely ill patients and those with abnormal CRP and d-dimer levels. Data regarding the quality of antibiotic prescribing were lacking.

Background The SARS-CoV-2 primarily enters into the human body through nasopharyngeal tract (NT) and is the etiological agent of COVID-19. The microbiota of the NT may play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. To shed light on the effects and consequences of SARS-CoV-2 infection on microbiome diversity and composition, we conducted a high throughput RNA-Seq metagenomic investigation of 22 NT swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7). Results This study for the first time demonstrates the association of microbiome diversity and their concomitant genomic features in the NT of COVID-19 and Recovered patients compared to Healthy humans, and discusses the role of the altered microbiomes in the pathophysiology of the SARS-CoV-2 infections. Our RNA-Seq metagenomic analyses detected 2281 bacterial species (including 1477, 919 and 676 in samples of Healthy human, COVID-19 and Recovered patients, respectively) indicating a distinct microbiome dysbiosis (COVID-19>Recovered>Healthy). The samples from COVID-19 patients and Recovered individuals had inclusion of 67% (including Streptococcus salivarius, S. mitis, Neisseria subflava, Veillonella dispar, Acinetobacter junii, Prevotella melaninogenica etc.) and 77% (including Pseudomonas stutzeri, Staphylococcus capitis, S. epidermidis, P. mendocina, Moraxella osloensis, A. indicus, Escherichia coli etc.) opportunistic pathogenic bacteria, respectively compared to Healthy individuals. Notably, 79% commensal bacteria (e.g., Pseudomonas sp. LPH1, Brevundimonas sp. Bb-A, P. oleovorans, Pseudomonas sp. phDV1, Brevundimonas sp. DS20, Idiomarinaceae bacterium HL-53, Alishewanella sp. 205, Sphingobacterium psychroaquaticum etc.) were found in healthy individuals but not detected in COVID-19 patients and Recovered individuals. Similar dysbiosis was also found in viral and archaeal fraction of the microbiomes. Although, 55 viral and 48 archaeal genera were detected, only 16% viral and 27% archaeal genera were shared across three metagenomes. We also detected altered metabolic pathways and functional genes including resistance to antibiotics and toxic compounds in the pathophysiology of COVID-19.Conclusions The nasopharyngeal microbiome dysbiosis and their genomic features in COVID-19, Recovered and Healthy individuals determined by our RNA-Seq analyses shed light on early interactions of SARS-CoV-2 with the nasopharyngeal resident microbiota that might be helpful for developing microbiome-based diagnostics and therapeutics for this novel pandemic disease.

We report the sequencing of three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Bangladesh. We have identified a unique mutation (NSP2_V480I) in one of the sequenced genomes (isolate hCoV-19/Bangladesh/BCSIR-NILMRC-006/2020) compared to the sequences available in the Global Initiative on Sharing All Influenza Data (GISAID) database. The data from this analysis will contribute to advancing our understanding of the epidemiology of SARS-CoV-2 in Bangladesh as well as worldwide at the molecular level and will identify potential new targets for interventions.