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Otun Saha
Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh

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Review
Published: 13 August 2021 in COVID
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Concurrent waves of coronavirus disease, Ebola virus disease, avian influenza A, and black fungus are jeopardizing lives in some parts of Africa and Asia. From this point of view, this review aims to summarize both the socio-economic and public health implications of these parallel outbreaks along with their best possible management approaches. Online databases (PubMed/PMC/Medline, Publons, ResearchGate, Scopus, Google Scholar, etc.) were used to collect the necessary information regarding these outbreaks. Based on the reports published and analyses performed so far, the long-lasting impacts caused by these simultaneous outbreaks on global socio-economical and public health status can be conceived from the past experiences of outbreaks, especially the COVID-19 pandemic. Moreover, prolonged restrictions by the local government may lead to food insecurity, global recession, and an enormous impact on the mental health of people of all ages, specifically in developing countries. Such overwhelming effects have already been reported to be declining the national growth of the economy as well as increasing political insecurity and shortage of basic needs. Although various actions have already been taken, including vaccination, clinical management and further research, social distancing, lockdown, etc., to improve the situation, the emerging variants and associated genetic mutations may make containment difficult, worsening the situation again. So, considering the current mutational dynamics of the pathogens and past experiences, perpetual preparedness along with updated clinical management backed by epidemiological studies and innovative scientific effort are inevitable to combat the simultaneous waves of multiple infectious diseases.

ACS Style

Afroza Khan; Nayeema Talukder Ema; Nadira Naznin Rakhi; Otun Saha; Tamer Ahamed; Mizanur Rahaman. Parallel Outbreaks of Deadly Pathogens (SARS-CoV-2, H5N8, EVD, Black Fungi) around East Africa and Asia in 2021: Priorities for Outbreak Management with Socio-Economic and Public Health Impact. COVID 2021, 1, 203 -217.

AMA Style

Afroza Khan, Nayeema Talukder Ema, Nadira Naznin Rakhi, Otun Saha, Tamer Ahamed, Mizanur Rahaman. Parallel Outbreaks of Deadly Pathogens (SARS-CoV-2, H5N8, EVD, Black Fungi) around East Africa and Asia in 2021: Priorities for Outbreak Management with Socio-Economic and Public Health Impact. COVID. 2021; 1 (1):203-217.

Chicago/Turabian Style

Afroza Khan; Nayeema Talukder Ema; Nadira Naznin Rakhi; Otun Saha; Tamer Ahamed; Mizanur Rahaman. 2021. "Parallel Outbreaks of Deadly Pathogens (SARS-CoV-2, H5N8, EVD, Black Fungi) around East Africa and Asia in 2021: Priorities for Outbreak Management with Socio-Economic and Public Health Impact." COVID 1, no. 1: 203-217.

Journal article
Published: 10 August 2021 in Microorganisms
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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swamped the global environment greatly in the current pandemic. Wastewater-based epidemiology (WBE) effectively forecasts the surge of COVID-19 cases in humans in a particular region. To understand the genomic characteristics/footprints and diversity of SARS-CoV-2 in the environment, we analyzed 807 SARS-CoV-2 sequences from 20 countries deposited in GISAID till 22 May 2021. The highest number of sequences (n = 638) were reported in Austria, followed by the Netherlands, China, and Bangladesh. Wastewater samples were highest (40.0%) to successfully yield the virus genome followed by a 24 h composite wastewater sample (32.6%) and sewage (18.5%). Phylogenetic analysis revealed that SARS-CoV-2 environmental strains are a close congener with the strains mostly circulating in the human population from the same region. Clade GRY (32.7%), G (29.2%), GR (25.3%), O (7.2%), GH (3.4%), GV (1.4%), S (0.5%), and L (0.4%) were found in environmental samples. Various lineages were identified in environmental samples; nevertheless, the highest percentages (49.4%) of the alpha variant (B.1.1.7) were detected in Austria, Liechtenstein, Slovenia, Czech Republic, Switzerland, Germany, and Italy. Other prevalent lineages were B.1 (18.2%), B.1.1 (9.2%), and B.1.160 (3.9%). Furthermore, a significant number of amino acid substitutions were found in environmental strains where the D614G was found in 83.8% of the sequences. However, the key mutations—N501Y (44.6%), S982A (44.4%), A570D (43.3%), T716I (40.4%), and P681H (40.1%) were also recorded in spike protein. The identification of the environmental belvedere of SARS-CoV-2 and its genetic signature is crucial to detect outbreaks, forecast pandemic harshness, and prepare with the appropriate tools to control any impending pandemic. We recommend genomic environmental surveillance to trace the emerging variants and diversity of SARS-CoV-2 viruses circulating in the community. Additionally, proper disposal and treatment of wastewater, sewage, and medical wastes are important to prevent environmental contamination.

ACS Style

Ariful Islam; Abu Sayeed; Abul Kalam; Jinnat Ferdous; Kaisar Rahman; Josefina Abedin; Shariful Islam; Shahanaj Shano; Otun Saha; Tahmina Shirin; Mohammad Hassan. Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. Microorganisms 2021, 9, 1696 .

AMA Style

Ariful Islam, Abu Sayeed, Abul Kalam, Jinnat Ferdous, Kaisar Rahman, Josefina Abedin, Shariful Islam, Shahanaj Shano, Otun Saha, Tahmina Shirin, Mohammad Hassan. Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. Microorganisms. 2021; 9 (8):1696.

Chicago/Turabian Style

Ariful Islam; Abu Sayeed; Abul Kalam; Jinnat Ferdous; Kaisar Rahman; Josefina Abedin; Shariful Islam; Shahanaj Shano; Otun Saha; Tahmina Shirin; Mohammad Hassan. 2021. "Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally." Microorganisms 9, no. 8: 1696.

Original paper
Published: 12 July 2021 in Virus Genes
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Along with intrinsic evolution, adaptation to selective pressure in new environments might have resulted in the circulatory SARS-CoV-2 strains in response to the geoenvironmental conditions of a country and the demographic profile of its population. With this target, the current study traced the evolutionary route and mutational frequency of 198 Bangladesh-originated SARS-CoV-2 genomic sequences available in the GISAID platform over a period of 13 weeks as of 14 July 2020. The analyses were performed using MEGA X, Swiss Model Repository, Virus Pathogen Resource and Jalview visualization. Our analysis identified that majority of the circulating strains strikingly differ from both the reference genome and the first sequenced genome from Bangladesh. Mutations in nonspecific proteins (NSP2-3, NSP-12(RdRp), NSP-13(Helicase)), S-Spike, ORF3a, and N-Nucleocapsid protein were common in the circulating strains with varying degrees and the most unique mutations (UM) were found in NSP3 (UM-18). But no or limited changes were observed in NSP9, NSP11, Envelope protein (E) and accessory factors (NSP7a, ORF 6, ORF7b) suggesting the possible conserved functions of those proteins in SARS-CoV-2 propagation. However, along with D614G mutation, more than 20 different mutations in the Spike protein were detected basically in the S2 domain. Besides, mutations in SR-rich region of N protein and P323L in RDRP were also present. However, the mutation accumulation showed a significant association (p = 0.003) with sex and age of the COVID-19-positive cases. So, identification of these mutational accumulation patterns may greatly facilitate vaccine development deciphering the age and the sex-dependent differential susceptibility to COVID-19.

ACS Style

Otun Saha; Israt Islam; Rokaiya Nurani Shatadru; Nadira Naznin Rakhi; Shahadat Hossain; Mizanur Rahaman. Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Virus Genes 2021, 1 -13.

AMA Style

Otun Saha, Israt Islam, Rokaiya Nurani Shatadru, Nadira Naznin Rakhi, Shahadat Hossain, Mizanur Rahaman. Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Virus Genes. 2021; ():1-13.

Chicago/Turabian Style

Otun Saha; Israt Islam; Rokaiya Nurani Shatadru; Nadira Naznin Rakhi; Shahadat Hossain; Mizanur Rahaman. 2021. "Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh." Virus Genes , no. : 1-13.

Preprint
Published: 14 June 2021
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Concurrent waves of Coronavirus disease, Ebola virus disease, avian influenza A and black fungus are jeopardizing the lives in some parts of Africa and Asia. From this point of view, this review aims to summarize both socio-economic and public health implications of these parallel outbreaks along with their best possible management approaches. Various online databases were used to collect the necessary information regarding these outbreaks. Based on the reports published and analyses done so far, the long-lasting damages caused by these simultaneous outbreaks on global socio-economical and public health status can be conceived from the past experiences of outbreaks, especially the COVID-19 pandemic. Moreover, prolonged restrictions by the local government may lead to food insecurity, global recession, and an enormous impact on the mental health of people of all ages, specifically in developing countries. Such overwhelming effects already have been reported to be declining national growth of the economy as well as increasing political insecurity and shortage of basic needs. Although various actions have already been taken including vaccination, clinical management, and further research, social distancing, and lockdown, etc. to improve the situation, the emerging variants and associated genetic mutations may make the containment difficult worsening the situation again. Considering the current mutational dynamics of the pathogens and the past experiences, perpetual preparedness along with updated clinical management backed by epidemiological studies and innovating scientific effort are inevitable to combat the simultaneous waves of multiple infectious diseases.

ACS Style

Afroza Khan; Nayeema Talukde Ema; Nadira Naznin Rakhi; Otun Saha; Mizanur Rahaman. Parallel Outbreaks of Deadly Pathogens (SARS-CoV-2, H5N8, EVD, Black fungi) around the World in 2021: Priorities for Achieving Control with Socio-Economic and Public Health Impact. 2021, 1 .

AMA Style

Afroza Khan, Nayeema Talukde Ema, Nadira Naznin Rakhi, Otun Saha, Mizanur Rahaman. Parallel Outbreaks of Deadly Pathogens (SARS-CoV-2, H5N8, EVD, Black fungi) around the World in 2021: Priorities for Achieving Control with Socio-Economic and Public Health Impact. . 2021; ():1.

Chicago/Turabian Style

Afroza Khan; Nayeema Talukde Ema; Nadira Naznin Rakhi; Otun Saha; Mizanur Rahaman. 2021. "Parallel Outbreaks of Deadly Pathogens (SARS-CoV-2, H5N8, EVD, Black fungi) around the World in 2021: Priorities for Achieving Control with Socio-Economic and Public Health Impact." , no. : 1.

Short communication
Published: 01 November 2020 in Gene Reports
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new strain of beta coronavirus that has spread worldwide within a short period of time and has been responsible for the current COVID-19 pandemic. This novel virus shows high transmission and adaptability frequency into the host with rapid changes in genomic sequences. In this study, we analyzed the complete genome of 41 strains isolated in Bangladesh to understand the evolutionary route and genetic variations of this rapidly evolving virus. The phylogenetics, parsimony informative sites and mutation analyses were performed using MEGA X, Multiple sequence alignment program (MAFFT), and Virus Pathogen Resource. The phylogenetic analysis of the studied genomes along with the reference genome suggested that the viral strains found in Bangladesh might be coming from multiple countries such as France, Germany, India, the USA, and Brazil. After entering into the country, intra-cluster and inter-cluster began to circulate in the 8 individual divisions of Bangladesh. We also identified 26 parsimony-informative sites along with the 9 most important sites for virus evolution. Genome-wide annotations revealed 256 mutations, of which 10 were novel (NSP3, RdRp, Spike) in Bangladeshi strains where I120F(NSP2), P323L(RdRp), D614G (Spike), R203K, G204R(N) are the most prominent. Most importantly, numerous mutations were flourishing in the N protein gene (67) followed by S (45), RdRp (38), NSP2 (34), NSP3 (20), and ORF8 (6) gene. Moreover, nucleotide deletion analysis found nine deletions throughout the genomes including in ORF7a (8), ORF8 (1) with one insertion (G) at 265 positions in only one genome. The underlying mechanism of disease severity, molecular evolution, and epidemiology lie in genomic sequences that are not fully understood yet. Identification of the evolutionary history, parsimony-informative sites and others genetic variations of this deadly virus will facilitate the development of new strategies to control the local transmission and provide deep insight in the identification of potential therapeutic targets for controlling COVID-19.

ACS Style

Otun Saha; Shahadat Hossain; Mizanur Rahaman. Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh. Gene Reports 2020, 21, 100951 -100951.

AMA Style

Otun Saha, Shahadat Hossain, Mizanur Rahaman. Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh. Gene Reports. 2020; 21 ():100951-100951.

Chicago/Turabian Style

Otun Saha; Shahadat Hossain; Mizanur Rahaman. 2020. "Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh." Gene Reports 21, no. : 100951-100951.

Preprint content
Published: 21 August 2020
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Along with intrinsic evolution, adaptation to selective pressure in new environments might have resulted in the circulatory SARS-CoV-2 strains in response to the geoenvironmental conditions of a country and the demographic profile of its population. Thus the analysis of genomic mutations of these circulatory strains may give an insight into the molecular basis of SARS-CoV-2 pathogenesis and evolution favoring the development of effective treatment and containment strategies. With this target, the current study traced the evolutionary route and mutational frequency of 198 Bangladesh originated SARS-CoV-2 genomic sequences available in the GISAID platform over a period of 13 weeks as of 14 July 2020. The analyses were performed using MEGA 7, Swiss Model Repository, Virus Pathogen Resource and Jalview visualization. Our analysis identified that majority of the circulating strains in the country belong to B and/or L type among cluster A to Z and strikingly differ from both the reference genome and the first sequenced genome from Bangladesh. Mutations in Nonspecific protein 2 (NSP2), NSP3, RNA dependent RNA polymerase (RdRp), Helicase, Spike, ORF3a, and Nucleocapsid (N) protein were common in the circulating strains with varying degrees and the most unique mutations(UM) were found in NSP3 (UM-18). But no or limited changes were observed in NSP9, NSP11, E (Envelope), NSP7a, ORF 6, and ORF 7b suggesting the possible conserved functions of those proteins in SARS-CoV-2 propagation. However, along with D614G mutation, more than 20 different mutations in the Spike protein were detected basically in the S2 domain. Besides, mutations in SR-rich region of N protein and P323L in RDRP were also present. However, the mutation accumulation showed an association with sex and age of the COVID-19 positive cases. So, identification of these mutational accumulation patterns may greatly facilitate drug/ vaccine development deciphering the age and the sex dependent differential susceptibility to COVID-19.

ACS Style

Otun Saha; Rokaiya Nurani Shatadru; Nadira Naznin Rakhi; Israt Islam; Shahadat Hossain; Mizanur Rahaman. Temporal landscape of mutation accumulation in SARS-CoV-2 genomes from Bangladesh: possible implications from the ongoing outbreak in Bangladesh. 2020, 1 .

AMA Style

Otun Saha, Rokaiya Nurani Shatadru, Nadira Naznin Rakhi, Israt Islam, Shahadat Hossain, Mizanur Rahaman. Temporal landscape of mutation accumulation in SARS-CoV-2 genomes from Bangladesh: possible implications from the ongoing outbreak in Bangladesh. . 2020; ():1.

Chicago/Turabian Style

Otun Saha; Rokaiya Nurani Shatadru; Nadira Naznin Rakhi; Israt Islam; Shahadat Hossain; Mizanur Rahaman. 2020. "Temporal landscape of mutation accumulation in SARS-CoV-2 genomes from Bangladesh: possible implications from the ongoing outbreak in Bangladesh." , no. : 1.

Journal article
Published: 27 July 2020 in Microorganisms
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The avian pathogenic Escherichia coli (APEC) strains are the chief etiology of colibacillosis worldwide. The present study investigated the circulating phylotypes, existence of virulence genes (VGs), and antimicrobial resistance (AMR) in 392 APEC isolates, obtained from 130 samples belonged to six farms using both phenotypic and PCR-based molecular approaches. Congo red binding (CRB) assay confirmed 174 APEC isolates which were segregated into ten, nine, and eight distinct genotypes by RAPD assay (discriminatory index, DI = 0.8707), BOX-PCR (DI = 0.8591) and ERIC-PCR (DI = 0.8371), respectively. The combination of three phylogenetic markers (chuA, yjaA and DNA fragment TspE4.C2) classified APEC isolates into B23 (37.36%), A1 (33.91%), D2 (11.49%), B22 (9.20%), and B1 (8.05%) phylotypes. Majority of the APEC isolates (75–100%) harbored VGs (ial, fimH, crl, papC, and cjrC). These VGs (papC and cjrC) and phylotypes (D2 and B2) of APEC had significant (p = 0.004) association with colibacillosis. Phylogenetic analysis showed two distinct clades (clade A and clade B) of APEC, where clade A had 98%–100% similarity with E. coli APEC O78 and E. coli EHEC strains, and clade B had closest relationship with E. coli O169:H41 strain. Interestingly, phylogroups B2 and D2 were found in the APEC strains of both clades, while the strains from phylogroups A1 and B1 were found in clade A only. In this study, 81.71% of the isolates were biofilm formers, and possessed plasmids of varying ranges (1.0 to 54 kb). In vitro antibiogram profiling revealed that 100% isolates were resistant to ≥3 antibiotics, of which 61.96%, 55.24%, 53.85%, 51.16% and 45.58% isolates in phylotypes B1, D2, B22, B23, and A1, respectively, were resistant to these antimicrobials. The resistance patterns varied among different phylotypes, notably in phylotype B22, showing the highest resistance to ampicillin (90.91%), nalidixic acid (90.11%), tetracycline (83.72%), and nitrofurantoin (65.12%). Correspondence analysis also showed significant correlation among phylotypes with CRB (p = 0.008), biofilm formation (p = 0.02), drug resistance (p = 0.03), and VGs (p = 0.06). This report demonstrated that B2 and A1 phylotypes are dominantly circulating APEC phylotypes in Bangladesh; however, B2 and D2 are strongly associated with the pathogenicity. A high prevalence of antibiotic-resistant APEC strains from different phylotypes suggest the use of organic antimicrobial compounds, and/or metals, and the rotational use of antibiotics in poultry farms in Bangladesh.

ACS Style

Otun Saha; M. Hoque; Ovinu Islam; Mizanur Rahaman; Munawar Sultana; M. Hossain. Multidrug-Resistant Avian Pathogenic Escherichia coli Strains and Association of Their Virulence Genes in Bangladesh. Microorganisms 2020, 8, 1135 .

AMA Style

Otun Saha, M. Hoque, Ovinu Islam, Mizanur Rahaman, Munawar Sultana, M. Hossain. Multidrug-Resistant Avian Pathogenic Escherichia coli Strains and Association of Their Virulence Genes in Bangladesh. Microorganisms. 2020; 8 (8):1135.

Chicago/Turabian Style

Otun Saha; M. Hoque; Ovinu Islam; Mizanur Rahaman; Munawar Sultana; M. Hossain. 2020. "Multidrug-Resistant Avian Pathogenic Escherichia coli Strains and Association of Their Virulence Genes in Bangladesh." Microorganisms 8, no. 8: 1135.

Preprint content
Published: 01 July 2020
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The avian pathogenic Escherichia coli (APEC) strains are the chief etiology of avian colibacillosis worldwide. The present study investigated the circulating phylotypes, existence of virulence genes (VGs) and antimicrobial resistance (AMR) in 392 APEC isolates, obtained from 130 samples belonged to six farms using both phenotypic and PCR-based molecular approaches. Congo red binding (CRB) assay confirmed 174 APEC isolates which were segregated into 10, 9 and 8 distinctive genotypes by RAPD assay (discriminatory index, D=0.8707), BOX-PCR (D=0.8591) and ERIC-PCR (D=0.8371), respectively. The combination of three phylogenetic markers (chuA, yjaA and DNA fragment TspE4.C2) classified APEC isolates into B23 (37.36%), A1 (33.91%), D2 (11.49%), B22 (9.20%) and B1 (8.05%) phylotypes. Majority of the APEC isolates (75-100%) harbored VGs (ial, fimH, crl, papC and cjrC), and of them, VGs (papC and cjrC) and phylotypes (D2 and B2) of APEC had significant (p=0.004) association with colibacillosis. Phylogenetic analysis showed two distinct clades (Clade A and Clade B) of APEC where Clade A had 98-100.0% similarity with E. coli APEC O78 and E. coli EHEC strains, and Clade B had closest relationship with E. coli O169:H41 strain. Interestingly, phylogroups B2 and D2 were found in the APEC strains of both clades while the strains from phylogroups A1 and B1 were found in clade A only. In this study, 81.71% of the isolates were biofilm formers and possessed plasmids of varying ranges (1.0 to 54 kb). In vitro antibiogram profiling revealed that 100.0% isolates were resistant to ≥3 antibiotics, of which61.96%, 55.24, 53.85, 51.16 and 45.58 % isolates in phylotypes B1, D2, B22, B23 and A1, respectively were these antimicrobials. The resistance patterns varied among different phylotypes, notably in phylotype B22 showing the highest resistance to ampicillin (90.91%), nalidixic acid (90.11%), tetracycline (83.72%) and nitrofurantoin (65.12%). Correspondence analysis also showed significant correlation of phylotypes with CRB (p=0.008), biofilm formation (p=0.02), drug resistance (p=0.03) and VGs (p=0.06). This report demonstrated that B2 and A1 phylotypes are dominantly circulating APEC phylotypes in Bangladesh; however, B2 and D2 are strongly associated with the pathogenicity. A high prevalence of antibiotic resistant APEC strains from different phylotypes suggest to use of organic antimicrobial compounds, and/or metals, and the rotational use of antibiotics in the poultry farms in Bangladesh.

ACS Style

Otun Saha; M. Nazmul Hoque; Ovinu Kibria Islam; Mizanur Rahaman; Munawar Sultana; M. Anwar Hossain. Multidrug-Resistant Avian Pathogenic Escherichia coli Strains and Association of Their Virulence Genes in Bangladesh. 2020, 1 .

AMA Style

Otun Saha, M. Nazmul Hoque, Ovinu Kibria Islam, Mizanur Rahaman, Munawar Sultana, M. Anwar Hossain. Multidrug-Resistant Avian Pathogenic Escherichia coli Strains and Association of Their Virulence Genes in Bangladesh. . 2020; ():1.

Chicago/Turabian Style

Otun Saha; M. Nazmul Hoque; Ovinu Kibria Islam; Mizanur Rahaman; Munawar Sultana; M. Anwar Hossain. 2020. "Multidrug-Resistant Avian Pathogenic Escherichia coli Strains and Association of Their Virulence Genes in Bangladesh." , no. : 1.

Preprint content
Published: 31 March 2020
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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.

ACS Style

M. Shaminur Rahman; M. Nazmul Hoque; M. Rafiul Islam; Salma Akter; A. S. M. Rubayet-Ul-Alam; Mohammad Anwar Siddique; Otun Saha; Mizanur Rahaman; Munawar Sultana; M. Anwar Hossain. Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach. 2020, 1 .

AMA Style

M. Shaminur Rahman, M. Nazmul Hoque, M. Rafiul Islam, Salma Akter, A. S. M. Rubayet-Ul-Alam, Mohammad Anwar Siddique, Otun Saha, Mizanur Rahaman, Munawar Sultana, M. Anwar Hossain. Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach. . 2020; ():1.

Chicago/Turabian Style

M. Shaminur Rahman; M. Nazmul Hoque; M. Rafiul Islam; Salma Akter; A. S. M. Rubayet-Ul-Alam; Mohammad Anwar Siddique; Otun Saha; Mizanur Rahaman; Munawar Sultana; M. Anwar Hossain. 2020. "Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach." , no. : 1.

Preprint
Published: 04 November 2019
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The bovine clinical mastitis (CM) milk is a large reservoir for diverse groups of resistomes, which play important roles in the pathogenesis of mastitis, but little is known about the concurrence of CM microbiome signature and its associated resistomes. Here we deciphered the total resistance (antibiotics and metals resistance, biofilm formation, quorum sensing) present in CM microbiome using whole metagenome sequencing (WMS) and in vitro cultural approaches. Significant correlation (p=0.001) was found between the resistome diversity and microbiome signature. We identified the strain-level microbiome diversity in four cattle breeds, with microbiome composition represented by the phyla Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Fusobacteria (contributing to >95.0% of total strains). However, the resistome diversity did not vary significantly (p=0.692) across the microbiomes of cattle breeds. The in vitro investigation showed that biofilm producing CM pathogens were resistant to most of the conventional antibiotics used for CM treatment, whereas these pathogens remained sensitive to five heavy metals (Cr, Co, Ni, Cu, Zn) at varying concentrations. We also found association of some genomic functional potentials such as bacterial flagellar movement and chemotaxis, regulation and cell signaling, phages-prophages, transposable elements, plasmids and oxidative stress in the pathophysiology of bovine CM. These findings of rapid and reliable identification of CM microbiomes and associated resistomes will help improve the optimization of therapeutic schemes involving antibiotics and metals usage in the prevention and control programs of bovine CM.

ACS Style

M. Nazmul Hoque; Arif Istiaq; Rebecca A. Clement; Keylie M. Gibson; Otun Saha; Ovinu Kibria Islam; Ruhshan Ahmed Abir; Munawar Sultana; Amam Zonaed Siddiki; Keith A. Crandall; Anwar Hossain. Resistome diversity in bovine clinical mastitis microbiome, a signature concurrence. 2019, 829283 .

AMA Style

M. Nazmul Hoque, Arif Istiaq, Rebecca A. Clement, Keylie M. Gibson, Otun Saha, Ovinu Kibria Islam, Ruhshan Ahmed Abir, Munawar Sultana, Amam Zonaed Siddiki, Keith A. Crandall, Anwar Hossain. Resistome diversity in bovine clinical mastitis microbiome, a signature concurrence. . 2019; ():829283.

Chicago/Turabian Style

M. Nazmul Hoque; Arif Istiaq; Rebecca A. Clement; Keylie M. Gibson; Otun Saha; Ovinu Kibria Islam; Ruhshan Ahmed Abir; Munawar Sultana; Amam Zonaed Siddiki; Keith A. Crandall; Anwar Hossain. 2019. "Resistome diversity in bovine clinical mastitis microbiome, a signature concurrence." , no. : 829283.