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Foot-and-mouth disease virus (FMDV) serotype A exhibits a higher degree of genetic and antigenic diversity resulting in frequent vaccine failure due to serological mismatch between the vaccine and heterologous strains. Currently, knowledge on the molecular basis of antigenic relationships among the FMDVs is limited; nevertheless, intratype antigenic variation due to mutation(s) is widely considered as the main hurdle to appropriate FMD vaccine development. Here, we studied genetic and antigenic variations of four FMDV serotype A isolates, BAN/GA/Sa-197/2013 (BAN-197), BAN/CH/Sa-304/2016 (BAN-304), BAN/DH/Sa-307/2016 (BAN-307) and BAN/DH/Sa-310/2017 (BAN-310) circulating in Bangladesh during 2013-2017. Initially, antigenic relationships (r1 -values) of the field isolates were evaluated by the two-dimensional microneutralization test (2D-MNT) using the hyperimmune antisera raised in cattle against the vaccine strain, BAN-304. Interesingly, the results showed protective serological cross-reactivity (r1 -values > 0.4) between the vaccine strain and the field isolates, BAN-307 and BAN-310, except BAN-197 that substantially mismatched (r1 = 0.129 ± 0.043) with the BAN-304. Although VP1-based phylogeny grouped all the isolates within the same sublineage C (a subgroup of VP3Δ59 variant) under the lineage A/ASIA/G-VII, strikingly, computational analyses of the viral capsid proteins demonstrated significant deviation at the VP1 G-H loop of BAN-197 from the vaccine strain, while VP(2-4) of both isolates were structurally conserved. To bridge the gap of how the distortion of the G-H loop and consequent antigenic hetergeneity occurred in BAN-197, we performed in silico combinatorial substitutions of the VP1 mutant amino acids (aa) of BAN-197 with the respective residues in BAN-304. Remarkably, our analyses revealed that two substitutions of distantly located aa at B-C (T48I:threonine → isoleucine) and G-H (A143V:alanine → valine) loops, in combination, distorted the VP1 G-H loop. Overall, this work contributes to understanding the molecular basis of antigenic relationships operating in serotype A FMDVs and the selection of suitable vaccine strain(s) for effective prophylaxis of FMD based on VP1-based analyses.

One of the six sublineages of the dominant O/ME-SA/Ind2001 lineage of foot-and-mouth disease virus (FMDV), Ind2001BD1 has already spread throughout 14 countries, including Bangladesh. Here, we report the complete genome sequence of the potential serotype O vaccine strain BAN/TA/Dh-301/2016, which has been shown to provide protection against all the circulating serotype O viruses in Bangladesh. The viral genome is 8,211 nucleotide (nt) long with an open reading frame (ORF) of 6999 nt. The ORF is flanked by a 1098-nt-long 5'-UTR and a 114-nt-long 3'-UTR. Compared to the Indian FMDV serotype O vaccine strain O/India/R2/75 (AF204276), ten mutations were identified in the major antigenic sites of BAN/TA/Dh-301/2016 (MK088170.1).

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been considered with great importance on correct screening procedure. The detection efficiency of recent variants of concern were observed by comparing 5 commercial RT-PCR kits and a SYBR-green method developed and validated in our laboratory. The RNA was extracted from nasopharyngeal samples from suspected COVID-19 patients and RT-PCR assay was performed according to the instruction of the respective manufacturers. The specificity and sensitivity of Maccura kit was 81.8% and 82.5%, A*Star kit was 100% and 75.4%, Da An Gene kit was 100% and 68.4%, Sansure kit was 54.5% and 91.2% and TaqPath kit was 100% and 70.2% respectively. Our in house SYBR-Green method showed a consistent detection result with 90.9% specificity and 91.2% sensitivity. We also found that detection kits targeting more genes showed better accuracy which facilitates less false positive results (

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has evolved into eight fundamental clades with four of these clades (G, GH, GR, and GV) globally prevalent in 2020. To explain plausible epistatic effects of the signature co‐occurring mutations of these circulating clades on viral replication and transmission fitness, we proposed a hypothetical model using in silico approach. Molecular docking and dynamics analyses showed the higher infectiousness of a spike mutant through more favorable binding of G614 with the elastase‐2. RdRp mutation p.P323L significantly increased genome‐wide mutations (p, Highlights Most dominant spike mutation favors elastase‐2 binding.The polymerase mutant (P323L) virus may speed up replication that corresponds to higher mutations.ORF3a viroporin substitution (Q57H) decreases ion permeability.N protein mutation (RG203‐204KR) can increase nucleocapsid stability and help evade immunity.Co‐occurring mutations might modulate viral replication and transmission fitness through epistasis.

Raw milk contains wide microbial diversity, composed mainly of lactic acid bacteria (LAB), which are used as probiotics in both human and animal husbandry. We isolated, characterized, and evaluated LAB from indigenous Bangladeshi raw milk to assess probiotic potential, including antagonistic activity (against Escherichia coli O157: H7, Enterococcus faecalis, Salmonella Typhimurium, Salmonella Enteritidis, and Listeria monocytogenes), survivability in simulated gastric juice, tolerance to phenol and bile salts, adhesion to ileum epithelial cells, auto- and co-aggregation, hydrophobicity, α-glucosidase inhibitory activity, and antibiotic susceptibility tests. The 4 most promising LAB strains showed probiotic potential and were identified as Lactobacillus casei, Lactobacillus plantarum (which produced plantaricin EF), Lactobacillus fermentum, and Lactobacillus paracasei. These strains inhibited all pathogens tested at various degrees, and competitively excluded pathogens with viable counts of 3.0 to 6.0 log cfu/mL. Bacteriocin, organic acids, and low-molecular-weight substances were mainly responsible for antimicrobial activity by the LAB strains. All 4 LAB strains were resistant to oxacillin and 3 were resistant to vancomycin and streptomycin, with multiple antibiotic resistance indices >0.2. After further in vivo evaluation, these LAB strains could be considered probiotic candidates with application in the food industry.

Foot-and-mouth disease virus (FMDV) is a highly evolutionary divergent pathogen causing great economic havoc in many countries. Among its seven existing serotypes, Asia1 is the least divergent with a single topotype both genetically and antigenically. It is reported sporadically in Indian subcontinent and was classified under lineage G-VIII. In 2018, serotype Asia1 re-emerged in Bangladesh after 2013, along with circulation of a novel serotype Asia1 BD-18 (G-IX) lineage. VP1 phylogeny and sequence variation clearly demonstrated the novel strains which was estimated to have at least >5% nucleotide divergence with distinct clade formation. Also, the Bayesian phylogeographic inferences traced back to the origin time of lineage G-IX in early 2017 and a possible origin in Bangladesh. Mutational analysis considering established eight lineages revealed that the virus strains belonged to lineage G-IX contained a unique mutation at 44 position in the B-C loop region of VP1. Inappropriate vaccination and inefficient outbreak surveillance possibly contributed to the current episode of emergence. Therefore, active surveillance and continued vigilance are essential to assess and timely detect the occurrence, extent and distribution of this novel Asia1 strains in Bangladesh and the neighbouring countries.

Global emergence and dissemination of carbapenemases are clinically threatening, notably in countries with endemic blaNDM. To analyze the extent of carbapenemases in Bangladesh, 71 isolates were collected from 7 different clinical sources: wound swab (n = 38), pus (n = 13), urine (n = 9), blood (n = 4), tracheal aspirate (n = 3), pleural fluid (n = 1) and vaginal swab (n = 3) from Dhaka Medical College Hospital, Bangladesh. Among the isolates, 25 were resistant to at least one of the three carbapenems (imipenem, meropenem and doripenem), including 15 being resistant to all. These resistant isolates were identified as Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, P. hibiscicola, Proteus mirabilis, Providencia stuartii and Citrobacter sedlakii. Carbapenemase detection among these 25 isolates varied in individual phenotypic assays (83% in Modified Hodge Test, 50% in Combined Disk Test for Metallo-β-lactamase prediction) as compared with the genotypes observed (96% prevalence of various carbapenemases including blaOXA-1,48, blaNDM-1,5, blaVIM-2,5). blaOXA-48 was the most prevalent gene (84%) followed by blaNDM (72%). Coexistence of multiple gene combination such as blaNDM+blaOXA-48+blaOXA-1 was prevalent (48%). Harborage of blaVIM-5 (n = 1) was characterized for the first time, while blaNDM-5 (n = 5) was reported contemporarily with a recent study in Bangladesh. Presence of plasmids (64%) and integron class 1 (100%) signifies the transferable potential of resistant traits. The emergence of such new variants along with the presence of the mobile genetic elements demands strict surveillance and combating strategies.

TaqMan probe-based commercial real-time (RT) PCR kits are expensive but most frequently used in COVID-19 diagnosis. The unprecedented scale of SARS-CoV-2 infections needs to meet the challenge of testing more persons at a reasonable cost. This study developed a simple and cost-effective alternative diagnostic method based on melting curve analysis of SYBR green multiplex assay targeting two virus-specific genes along with a host-specific internal control. A total of 180 randomly selected samples portioning into two subsets based on crude and high-quality RNA extraction were used to compare this assay with a nationwide available commercial kit (Sansure Biotech Inc., (Hunan, China)), so that we could analyze the variation and validity of this in-house developed method. Our customized-designed primers can specifically detect the viral RNA likewise Sansure. We separately optimized SYBR Green RT-PCR reaction of N, E, S, and RdRp genes based on singleplex melting curve analysis at the initial stage. After several rounds of optimization on multiplex assays of different primer combinations, the optimized method finally targeted N and E genes of the SARS-CoV-2 virus, together with the β-actin gene of the host as an internal control. Comparing with the Sansure commercial kit, our proposed assay provided up to 97% specificity and 93% sensitivity. The cost of each sample processing ranged between ~2 and ~6 USD depending on the purification level of extracted RNA template. Overall, this one-step and one-tube method can revolutionize the COVID-19 diagnosis in low-income countries.

Arsenotrophic bacteria play an essential role in lowering arsenic contamination by converting toxic arsenite [As (III)] to less toxic and less bio-accumulative arsenate [As (V)]. The current study focused on the qualitative and electrocatalytic detection of the arsenite oxidation potential of an arsenite-oxidizing bacteria A. xylosoxidans BHW-15 (retrieved from As-contaminated tube well water), which could significantly contribute to arsenic detoxification, accumulation, and immobilization while also providing a scientific foundation for future electrochemical sensor development. The minimum inhibitory concentration (MIC) value for the bacteria was 15 mM As (III). Scanning Electron Microscopy (SEM) investigation validated its intracellular As uptake capacity and demonstrated a substantial association with the MIC value. During the stationary phase, the strain’s As (III) transformation efficiency was 0.0224 mM/h. Molecular analysis by real-time qPCR showed arsenite oxidase (aioA) gene expression increased 1.6-fold in the presence of As (III) compared to the untreated cells. The immobilized whole-cell also showed As (III) conversion up to 18 days. To analyze the electrochemical oxidation in water, we developed a modified GCE/P-Arg/ErGO-AuNPs electrode, which successfully sensed and quantified conversion of As (III) into As (V) by accepting electrons; implying a functional As oxidase enzyme activity in the cells. To the best of our knowledge, this is the first report on the electrochemical observation of the As-transformation mechanism with Achromobactersp. Furthermore, the current work highlighted that our isolate might be employed as a promising candidate for arsenic bioremediation, and information acquired from this study may be helpful to open a new window for the development of a cost-effective, eco-friendly biosensor for arsenic species detection in the future.

BackgroundThe mortality of COVID-19 disease is very high among males or elderly or individuals having comorbidities with obesity, cardiovascular diseases, lung infections, hypertension, and/or diabetes. Our study characterizes SARS-CoV-2 infected patients’ metagenomic features with or without type 2 diabetes to identify the microbial interactions associated with its fatal consequences.MethodThis study compared the baseline nasopharyngeal microbiome of SARS-CoV-2 infected diabetic and non-diabetic patients with controls adjusted with age and gender. The mNGS were performed using Ion GeneStudio S5 Series and the data were analyzed by the Vegan-package in R.ResultsAll three groups possessed significant bacterial diversity and dissimilarity indexes (p0.6, pConclusionThe dysbiosis of the bacterial community might be linked with severe consequences of COVID-19 infected diabetic patients, although few probiotic strains inhibited numerous pathogens in the same pathological niches. This study suggested that the promotion of normal-flora and probiotics through dietary changes and reduction of excessive pro-inflammatory states by preventing pathogenic environment might lead to a better outcome for those co-morbid patients.

PurposeCellulase, due to its massive applicability, has been used in various industrial processes such as biofuels (bioethanol, triphasic biomethanation), agricultural and plant waste management, chiral separation, and ligand binding studies. The finding of a novel cellulase-producing bacterium will benefit the industries, which rely on yeast to produce cellulase in fermentation technology, because bacteria can easily be manipulated and fermented cost-effectively.MethodsCellulase enzyme-secreting bacteria were isolated from different regions of the world’s largest mangrove forests, Sundarbans in Bangladesh. Biochemical, morphological, and 16S rRNA identification protocol was followed to precisely characterize the bacterial strains.ResultWe have determined that the strain T2-D2 (Bacillussp.), E1-PT (Pseudomonassp.), and D1-PT (Pseudomonassp.) showed maximum endoglycolytic and strain C1-BT (Bacillussp.), E1-BT (Bacillussp.), and T-4 (E) showed relatively higher exoglycolytic activity during the test. So, it can be easily cultured at a normal temperature (97.7–99.5 °F). On the one hand, T2-D2 (Bacillussp.) and E1-PT (Pseudomonassp.) have shown the highest growth rate at pH 7 as it was neither acidic nor basic.ConclusionIt was concluded that the strain T2-D2 (Bacillussp.) and E1-PT (Pseudomonassp.) would be our target cellulolytic strains wherein the experimental isolates belonged to the Enterobacteriaceae, Psuedomonacea, Bacillacea, and Morganellacea family.

The emerged novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a global health crisis that warrants an accurate and detailed characterization of the rapidly evolving viral genome for understanding its epidemiology, pathogenesis, and containment. Here, we explored 61,485 sequences of the nucleocapsid (N) protein, a potent diagnostic and prophylactic target, for identifying the mutations to review their roles in real-time polymerase chain reaction based diagnosis and observe consequent impacts. Compared to the Wuhan reference strain, a total of 1034 unique nucleotide mutations were identified in the mutant strains (49.15%, n = 30,221) globally. Of these mutations, 367 occupy primer binding sites including the 3'-end mismatch to the primer-pair of 11 well-characterized primer sets. Noteworthily, CDC (USA) recommended the N2 primer set contained a lower mismatch than the other primer sets. Moreover, 684 amino acid (aa) substitutions were located across 317 (75.66% of total aa) unique positions including 82, 21, and 83 of those in the RNA binding N-terminal domain (NTD), SR-rich region, and C-terminal dimerization domain, respectively. Moreover, 11 in-frame deletions, mostly (n = 10) within the highly flexible linker region, were revealed, and the rest was within the NTD region. Furthermore, we predicted the possible consequence of high-frequency mutations (≥20) and deletions on the tertiary structure of the N protein. Remarkably, we observed that a high frequency (67.94% of mutated sequences) co-occuring mutations (R203K and G204R) destabilized and decreased overall structural flexibility. The N protein of SARS-CoV-2 comprises an average of 1.2 mutations per strain compared to 4.4 and 0.4 in Middle East respiratory syndrome-related coronavirus and SARS-CoV, respectively. Despite being proposed as the alternative target to spike protein for vaccine and therapeutics, the ongoing evolution of the N protein may challenge these endeavors, thus needing further immunoinformatics analyses. Therefore, continuous monitoring is required for tracing the ongoing evolution of the SARS-CoV-2 N protein in prophylactic and diagnostic interventions.

SummaryTracing the globally circulating SARS-CoV-2 mutants is essential for the outbreak alerts and far-reaching epidemiological surveillance. The available technique to identify the phylogenetic clades through high-throughput sequencing is costly, time-consuming, and labor-intensive that hinders the viral genotyping in low-income countries. Here, we propose a rapid, simple and cost-effective amplification-refractory mutation system (ARMS)-based multiplex reverse-transcriptase PCR assay to identify six distinct phylogenetic clades: S, L, V, G, GH, and GR. This approach is applied on 24 COVID-19 positive samples as confirmed by CDC approved real-time PCR assay for SARS-CoV-2. Our multiplex PCR is designed in a mutually exclusive way to identify V-S and G-GH-GR clade variants separately. The pentaplex assay included all five variants and the quadruplex comprised of the triplex variants alongside either V or S clade mutations that created two separate subsets. The procedure was optimized in the primer concentration (0.2-0.6 µM) and annealing temperature (56-60°C) of PCR using 3-5 ng/µl cDNA template synthesized upon random- and oligo(dT)-primer based reverse transcription. The different primer concentration for the triplex and quadruplex adjusted to different strengths ensured an even amplification with a maximum resolution of all targeted amplicons. The targeted Sanger sequencing further confirmed the presence of the clade-featured mutations with another set of our designed primers. This multiplex ARMS-PCR assay is sample, cost-effective, and convenient that can successfully discriminate the circulating phylogenetic clades of SARS-CoV-2.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is continuously spreading worldwide at an unprecedented scale in 2020. Within the first six months of the COVID-19 pandemic, it has evolved into six clades according to GISAID where three (G, GH, and GR) are now globally prevalent (>75%). Here we report the prevalence of these dominant clades, both individually and in combination, with disease progression and death-case scenario that leads to infer fitness of the SARS-CoV-2 by compromising its virulence. Unlike G or GH clades, the GR clade strains represent a significant negative association with the death-case ratio (R= -0.558, p=0.019). Docking analysis revealed the molecular scenario behind more infectiousness of S protein D614G mutation and reasoned more favorable binding of G614 with the elastase-2. Viral RNA-dependent-RNA-polymerase (RdRp) mutation p.P323L facilitated significantly higher (p

Foot-and-mouth disease (FMD) is an economically devastating disease of the livestock worldwide and caused by the FMD virus (FMDV), which has seven immunologically distinct serotypes (O, A, Asia1, C, and SAT1–SAT3). Studies suggest that VP2 is relatively conserved among three surface-exposed capsid proteins (VP1–VP3) of FMDV, but the level of conservation has not yet been reported. Here we analyzed the comparative evolutionary divergence of VP2 and VP1 to determine the level of conservation in VP2 at different hierarchical levels of three FMDV serotypes (O, A, and Asia1) currently circulating in Asia through an in-depth computational analysis of 14 compiled datasets and designed a consensus VP2 protein that can be used for the development of a serotype-independent FMDV detection tool. The phylogenetic analysis clearly represented a significant level of conservation in VP2 over VP1 at each subgroup level. The protein variability analysis and mutational study showed the presence of 67.4% invariant amino acids in VP2, with the N-terminal end being highly conserved. Nine inter-serotypically conserved fragments located on VP2 have been identified, among which four sites showed promising antigenicity value and surface exposure. The designed 130 amino acid long consensus VP2 protein possessed six surface-exposed B cell epitopes, which suggests the possible potentiality of the protein for the development of a serotype-independent FMDV detection tool in Asia. Conclusively, this is the first study to report the comparative evolutionary divergence between VP2 and VP1, along with proposing the possible potentiality of a designed protein candidate in serotype-independent FMDV detection.

The impact of the COVID-19 outbreak had devastating consequences globally with 20,675,770 affected and 749,061 dead. Despite different measures to restrict transmission, the death toll continues to rise. The SAARC group of countries comprising eight nations—Afghanistan, Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan and Sri Lanka, where 23.75% of the world population reside, implemented containment measures at different stages of the outbreak with varying consequences. In this review, we examined the onset and transmission of the virus in each country at an early stage and critically appraised their response with respect to their medical facilities for diagnosis and management. We found that countries that succeeded to contain the spread of COVID-19 were able to do so by prioritizing non-pharmaceutical interventions (e.g. early and stricter lockdowns). Currently, the epicentre of COVID-19 appears to be shifting to India (the largest SAARC nation), the death toll is likely to steeply increase if effective and aggressive measures are not taken urgently. The authors believe that authorities of each of the SAARC countries should act decisively and cooperatively as a matter of urgency increasing the regional collaboration in an eloquent and durative way.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionary divergent RNA virus, is responsible for the present devastating COVID-19 pandemic. To explore the genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. Genome-wide annotations revealed 1,516 nucleotide-level variations at different positions throughout the entire genome of SARS-CoV-2. Moreover, nucleotide (nt) deletion analysis found twelve deletion sites throughout the genome other than previously reported deletions at coding sequence of the ORF8 (open reading frame), spike, and ORF7a proteins, specifically in polyprotein ORF1ab (n = 9), ORF10 (n = 1), and 3´-UTR (n = 2). Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n = 744), demonstrating the viral proteins heterogeneous. Notably, residues of receptor-binding domain (RBD) showing crucial interactions with angiotensin-converting enzyme 2 (ACE2) and cross-reacting neutralizing antibody were found to be conserved among the analyzed virus strains, except for replacement of lysine with arginine at 378th position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). Furthermore, our results of the preliminary epidemiological data on SARS-CoV-2 infections revealed that frequency of aa mutations were relatively higher in the SARS-CoV-2 genome sequences of Europe (43.07%) followed by Asia (38.09%), and North America (29.64%) while case fatality rates remained higher in the European temperate countries, such as Italy, Spain, Netherlands, France, England and Belgium. Thus, the present method of genome annotation employed at this early pandemic stage could be a promising tool for monitoring and tracking the continuously evolving pandemic situation, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategies.

Recent outbreak of novel coronavirus and its rapid pandemic escalation in all over the world has drawn the attention to urgent need for effective drug development. However, due to prolonged vaccine and drug development procedure against a newly emerged devastating SARS-CoV-2 virus pathogen, repurposing of existing potential pertinent drug molecules would be preferable strategy to reduce mortality immediately and further development of new drugs to combat overall global Covid-19 crisis in all over the world. Herein, we have filtered 23 prospective drug candidates through literature review. Assessing evidences from molecular docking studies, it was clearly seen that, Epirubicin, Vapreotida, and Saquinavir exhibited better binding affinity against SARS-CoV-2 Main Protease than other drug molecules among the 23 potential inhibitors. However, 50 ns molecular dynamics simulation indicated the less mobile nature of the docked complex maintaining structural integrity. Our overall prediction findings indicate that Epirubicin, Vapreotida, and Saquinavir may inhibit COVID-19 by synergistic interactions in the active cavity and those results can pave the way in drug discovery although it has to be further validated by in-vitro and in-vivo investigations. Communicated by Ramaswamy H. Sarma

The novel coronavirus, SARS-CoV-2, causes the unfathomable pandemic in the history of humankind. Bangladesh is also a victim of this critical situation. To investigate the genomic features of the pathogen, the first complete genome of the virus has very recently been published. Therefore, the long awaiting questions regarding the possible origin and typing of the strain(s) can now be answered. Here, we endeavor to mainly discuss the published reports or online-accessed data (results) regarding those issues and presented a comprehensive picture of the typing of the virus alongside the probable origin of the sub-clade containing Bangladeshi strain. Our observation suggested that this strain might have originated from the United Kingdom (UK) or other European countries epidemiologically linked to the UK. According to different genotyping classification schemes, this strain belongs to A2a clade under G major clade, is of B and/or L type, and is a SARS-CoV-2a sub-strain. The complete genome data will surely increase in the forwarding days in Bangladesh. However, a mass regional sequencing approach targeting the partial or complete genome can link the epidemiological data and may help in further clinical interventions.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concerns declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomics was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M, and E proteins. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of ≥90.0% world population coverage for different ethnic groups. Molecular docking and dynamics simulation of the chimeric vaccine with the immune receptors (TLR3 and TLR4) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased IFN-γ and IL-2 cytokines. The codon optimization and mRNA secondary structure prediction revealed that the chimera is suitable for high-level expression and cloning. Overall, the constructed recombinant chimeric vaccine candidate demonstrated significant potential and can be considered for clinical validation to fight against this global threat, COVID-19.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionarily divergent RNA virus etiological agent of COVID-19, is responsible for present devastating pandemic respiratory illness. To explore the genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. Genome-wide annotations revealed 1,407 nucleotide-level mutations at different positions throughout the entire genome of SARS-CoV-2. Moreover, nucleotide deletion analysis found nine deletions throughout the genome, including in polyprotein (n=6), ORF10 (n=1) and 3´-UTR (n=2). Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n=722), making the viral proteins heterogeneous. Notably, residues of receptor-binding domain (RBD) having crucial interactions with angiotensin-converting enzyme 2 (ACE2), and cross-reacting neutralizing antibody were found to be conserved among the analyzed SARS-CoV-2 strains, except for replacement of Lysine with Arginine at 378 position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). Our method of genome annotation is a promising tool for monitoring and tracking the epidemic, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategy.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concern declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomic was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M and E proteins. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of ≥ 90.0% world population coverage for different ethnic groups. Molecular docking of the chimeric vaccine peptide with the immune receptors (TLR3 and TLR4) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased INF-γ and IL-2 cytokines. The codon optimization and mRNA secondary structure prediction revealed the chimera is suitable for high-level expression and cloning. Overall, the constructed recombinant chimeric vaccine candidate demonstrated significant potential and can be considered for clinical validation to fight against this global threat, COVID-19.

Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals throughout the world. The endemicity of this disease in Bangladesh has been causing high economic loss and an impediment to the full potential surge of livestock industries. In Bangladesh, vaccination using imported or locally produced FMD vaccines is the existing practice of controlling the disease, although vaccine failure cases are very common. Hence, to address the problem, the present study was envisaged to develop an effective FMD vaccine tailored to the circulating indigenous foot-and-mouth disease virus (FMDV) strains. Three local circulating FMDVs O/BAN/TA/Dh-301/2016 ( MK088170.1 ), A/BAN/CH/Sa-304/2016 ( MK088171.1 ) and Asia1/BAN/DH/Sa-318/2018 ( MH457186.1 ) isolates were selected as vaccine strains based on recent epidemiology, genetic and antigenic analyses. These serotype O, A and Asia1 vaccine strains showed strong antigenic relationship (r1 > 0.3) with 100% to 75% of the respective circulating viruses. The candidate viruses were successfully inactivated by 3.0 mM binary ethylenimine within 7–10 h after the onset of inactivation. Extrapolation of inactivation kinetics confirmed

The near-complete genome sequence of foot-and-mouth disease virus (FMDV) serotype A potential vaccine strain BAN/CH/Sa-304/2016 is reported here. Its genome revealed antigenic heterogeneity with the current Indian vaccine strain IND40/00, with four amino acid substitutions in antigenically critical sites of the VP1 protein.

The near-complete genome sequence of a foot-and-mouth disease virus (FMDV), strain O/ME-SA/Ind2001BD2, isolated exclusively from Bangladesh, is reported here. Amino acid substitutions at critical antigenic sites of the capsid were identified compared to the surface proteins of existing vaccine strain O/India/R2/75 and contemporary FMDV serotype O isolates of Bangladesh.

Originating at December 2019 in China, SARS-CoV-2 has emerged as the deadliest pandemic in the history of mankind. Along with direct contact and droplet contaminations, possibility of infections through contaminated surfaces and fomites are being investigated. In this study, we aim to assess the prevalence of SARS-CoV-2 viral RNA by real time one-step reverse transcriptase PCR on banknotes being circulating in Bangladesh. We also assessed the persistence of the virus on banknotes spiked with SARS-CoV-2 positive diluted human nasopharyngeal samples. Among the 425 banknote samples collected from different entities, 7.29% (n= 31) were tested positive for targeted genes. Twenty four representative positive samples were assessed for N gene fragments by conventional PCR and sequenced. All the samples carry viral RNA belonged to GR clade, the predominant circulating clade in Bangladesh. In the test of stability, the N gene was detected for up to 72 h on banknotes spiked with nasopharyngeal samples and CT values increases significantly with time (p

Stenotrophomonas maltophilia is an emerging opportunistic pathogen, and immunocompromised patients are at a higher risk of getting infected with this nosocomial bacterium. The biggest concern is its inherent resistance to most of the commonly used antibiotics, leaving a few options for treatment. Moreover, recent studies have reported the emergence of its resistance to trimethoprim/sulfamethoxazole (TMP/SMX), the drugs of choice against this pathogen. In this study, we employed a subtractive proteome analysis approach to identify new drug targets against Stenotrophomonas maltophilia K279a. We identified 56 proteins to be essential for the survival of this pathogen, 33 of which are exclusively involved in its metabolism. We identified their subcellular locations and performed broad-spectrum analysis, interactome analysis, and functional analysis. Drug targeting properties and docking energy showed that 29 out of 33 proteins have the potential to serve as potential new therapeutic targets, and four proteins (dCTP deaminase, NAD(P)H:quinone oxidoreductase, dihydroneopterin aldolase, and α, α-trehalose-phosphate synthase) bind with high affinity to already approved or experimental drugs. Based on the broad-spectrum analysis and interactome analysis, we identified NAD(P)H:quinone oxidoreductase, dCTP deaminase, Phosphotransferase, and ATP-dependent Clp protease adapter (ClpS) as the most potential therapeutic targets. Notably, phosphotransferase and ClpS are new targets, i.e., they do not interact with any experimental or approved drugs. Overall, our study will guide the development of new and effective drugs for the treatment of Stenotrophomonas maltophilia infection.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concerns declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomics was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M, and E proteins. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of ≥90.0% world population coverage for different ethnic groups. Molecular docking and dynamics simulation of the chimeric vaccine with the immune receptors (TLR3 and TLR4) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased IFN-γ and IL-2 cytokines. The codon optimization and mRNA secondary structure prediction revealed that the chimera is suitable for high-level expression and cloning. Overall, the constructed recombinant chimeric vaccine candidate demonstrated significant potential and can be considered for clinical validation to fight against this global threat, COVID-19.

‘Tubifex worms’ encompass extensive cryptic diversity that requires molecular characterization to confirm the species commonly found in Bangladesh including their lineages. Therefore, this study focused on the molecular characterization and phylogeny analysis at lineages level by sequencing the fragment of 16S rRNA and cytochrome c oxidase subunit I (COI) genes through standard cloning and sequencing techniques followed by phylogenetic characterization. All six isolates, belong to the genus Limnodrilus that is confirmed into two different species (L. hoffmeisteri and L. claparedianus-cervix) of the tubifex. The phylogenetic analysis estimated that the resident worms are under the same clade although transmissions from other countries might likely occur through different aquatic routes and birds. The drawbacks were the use of a complex colony rather than a single worm and taking representative isolates instead of all the positive amplicons for sequencing. However, this study is the first report of genetical confirmation of the genus Limnodrilus at lineage level from Bangladesh. Keywords: Tubifex, Phylogeny, Cytochrome oxidase, 16S rRNA, Bangladesh

The complete genome sequence of foot-and-mouth disease virus (FMDV) serotype Asia1 isolated from Bangladesh is reported here. Genome analysis revealed amino acid substitutions in the VP1 antigenic region and deletions in both the 5′ and 3′ untranslated regions (UTRs) compared to the genome of the existing vaccine strain (GenBank accession no. AY304994).