Published Article

1. Islam, M. A., Marzan, A. Al, Arman, M. S., Shahi, S., Sakif, T. I., Hossain, M., Islam, T., & Hoque, M. N. (2023). Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents. Scientific Reports, 13(1), 18644. https://doi.org/10.1038/s41598-023-45517-1

Article Metrics:

5-year impact factor: 4.9

Article Accesses: 2322

Citation Indexes: 2

Altmetric: 108

Contributions: Assisted in concept and methodology development by reviewing literature. Analyzed 5724 high-quality SARS-CoV-2 genomes (GISAID) from deceased patients using phylogenetic and mutation profiling tools. Conducted statistical analysis (SPSS, R) identifying significant mutation impacts (p < 0.05, FDR < 5%). Created figures (Adobe-Illustrator) and contributed to drafting and editing manuscript.

The identification of deleterious mutations in different variants of SARS-CoV-2 and their roles in the morbidity of COVID-19 patients has yet to be thoroughly investigated. To unravel the spectrum of mutations and their effects within SARS-CoV-2 genomes, we analyzed 5,724 complete genomes from deceased COVID-19 patients sourced from the GISAID database. This analysis was conducted using the Nextstrain platform, applying a generalized time-reversible model for evolutionary phylogeny. These genomes were compared to the reference strain (hCoV-19/Wuhan/WIV04/2019) using MAFFT v7.470. Our findings revealed that SARS-CoV-2 genomes from deceased individuals belonged to 21 Nextstrain clades, with clade 20I (Alpha variant) being the most predominant, followed by clade 20H (Beta variant) and clade 20J (Gamma variant). The majority of SARS-CoV-2 genomes from deceased patients (33.4%) were sequenced in North America, while the lowest percentage (0.98%) came from Africa.

2. Marzan, A. Al, Shahi, S., Arman, M. S., Hasan, M. Z., & Ghosh, A. (2023). Probing biological network in concurrent carcinomas and Type-2 diabetes for potential biomarker screening: An advanced computational paradigm. Advances in Biomarker Sciences and Technology, 5, 89–104. https://doi.org/10.1016/j.abst.2023.10.001

Article Metrics: Captured Readers: 19

Contributions: Reviewed literature to aid in concept and methodology. Acquired and curated datasets from NCBI GEO, ensuring quality and human sample inclusion. Identified gene expression patterns, characterized pathways, and unraveled protein-protein interactions. Investigated transcription factor and miRNA interactions, enhancing understanding of disease mechanisms. Contributed to drafting and manuscript editing, creating figures in Adobe Illustrator.

Type-2 diabetes mellitus (T2DM), the predominant form of diabetes in adults, is a co-morbid condition that exacerbates the severity of many other diseases, including cardiovascular disease, obesity, dyslipidemia, hypertension, and cancer. Among these, cancer is particularly concerning due to elevated mortality rates and a distinct lack of cost-effective therapeutic interventions. Identifying novel biomarkers for improved early cancer detection is imperative. Therefore, an integrated bioinformatics analysis was conducted to elucidate the co-morbid relationship between T2DM and five different types of cancer, namely bladder (BLCA), breast (BRCA), colon (CRC), liver (HCC), and prostate cancer (PRAD) and identification of novel biomarkers for early cancer detection in individuals with T2DM. A significant comorbid relationship was observed among T2DM, BLCA, and BRCA through gene expression and pathway enrichment analysis, while a moderate association was observed for between T2DM, and PRAD.

3. Jakariya, M., Ahmed, F., Islam, M. A., Al Marzan, A., Hasan, M. N., Hossain, M., Ahmed, T., Hossain, A., Reza, H. M., Hossen, F., Nahla, T., Rahman, M. M., Bahadur, N. M., Islam, M. T., Didar-ul-Alam, M., Mow, N., Jahan, H., Barceló, D., Bibby, K., & Bhattacharya, P. (2022). Wastewater-based epidemiological surveillance to monitor the prevalence of SARS-CoV-2 in developing countries with onsite sanitation facilities. Environmental Pollution, 311, 119679. https://doi.org/10.1016/j.envpol.2022.119679

Article Metrics:

Impact Factor: 8.9

Citation Indexes: 51,

Captured Readers: 66, Social Media Shares, Likes & Comments: 53

Contributions: Collected samples from wastewater, and was involved in extracting RNA, preparing cDNA library, as well as in performing qRT-PCR. Analyzed the derived data and visualized it with R programming. Involved in figure illustration (Adobe Illustrator, R), manuscript reviewing, and editing process.

Wastewater-based epidemiology (WBE) has emerged as a valuable approach for forecasting disease outbreaks in developed countries with a centralized sewage infrastructure. On the other hand, due to the absence of well-defined and systematic sewage networks, WBE is challenging to implement in developing countries like Bangladesh where most people live in rural areas. Identification of appropriate locations for rural Hotspot Based Sampling (HBS) and urban Drain Based Sampling (DBS) are critical to enable WBE based monitoring system. We investigated the best sampling locations from both urban and rural areas in Bangladesh after evaluating the sanitation infrastructure for forecasting COVID-19 prevalence. A total of 168 wastewater samples were collected from 14 districts of Bangladesh during each of the two peak pandemic seasons. RT-qPCR commercial kits were used to target ORF1ab and N genes. The presence of SARS-CoV-2 genetic materials was found in 98% (165/168) and 95% (160/168) wastewater

4. Islam, M. A., Shahi, S., Marzan, A. Al, Amin, M. R., Hasan, M. N., Hoque, M. N., Ghosh, A., Barua, A., Khan, A., Dhama, K., Chakraborty, C., Bhattacharya, P., & Wei, D.-Q. (2023). Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development. Frontiers in Pharmacology, 14. https://doi.org/10.3389/fphar.2023.1090717

Article Metrics:

Impact Factor: 5.6

Citation Indexes: 20

Total views: 3,299, Downloads: 991

Contributions: Filtered 214,459 SARS-CoV-2 sequences from GISAID, selecting 10,531 complete genomes for analysis. Conducted mutation analysis with NextClade, PredictSNP etc., predicted immune responses for B and T cells, and assessed mutation impacts on protein stability using DynaMut and mCSM-PPI2. Normalized data and validated (five-fold cross-validation) findings with machine learning classifiers.

Compared to the Wuhan-Hu-1 reference strain NC 045512.2, genome-wide annotations showed 16,954 mutations in the SARS-CoV-2 genome. We determined that the Omicron variant had 6,307 mutations (retrieved sequence:1947), including 67.8% unique mutations, more than any other variant evaluated in this study. The spike protein of the Omicron variant harboured 876 mutations, including 443 deleterious mutations. Among these deleterious mutations, 187 were common and 256 were unique non-synonymous mutations. In contrast, after analysing 1,884 sequences of the Delta variant, we discovered 4,468 mutations, of which 66% were unique, and not previously reported in other variants. Mutations affecting spike proteins are mostly found in RBD regions for Omicron, whereas most of the Delta variant mutations drawn to focus on amino acid regions ranging from 911 to 924 in the context of epitope prediction (B cell & T cell) and mutational stability impact data protruding that omicron is more transmissible.

5. Kabir, M. I., Chowdhury, S. A., Banik, B. K., Hoque, M. A., & Marzan, A. Al. (2023). Biosorption of pollutants from chemically derived wastewater using Microcoleus sp. AQUA — Water Infrastructure, Ecosystems and Society, 72(5), 750–761. https://doi.org/10.2166/aqua.2023.021

Article Metrics:

Impact Factor: 4.3

Citation Indexes: 1

Contributions: Contributed to microalgae sample preparation and experimental setup for synthetic wastewater treatment. Optimized environmental conditions and conducted batch experiments with varying doses and retention times. Analyzed data using spectrophotometry, calculated removal efficiency, and performed biosorption modeling. Involved in figure illustration (Adobe Illustrator, R), manuscript reviewing, and the editing process.

Microcoleus sp. is a versatile microorganism widely available in the environment and easily culturable. Hence, there is a progressing demand for wastewater treatment using this novel biosorption medium. The design of such a treatment method may be defined as an optimisation problem of algal dose and hydraulic retention time for attaining an adequate removal efficiency of heavy metals (Cr6+, Ni2+, and Zn2+) and nutrients (PO43- and NO3-). Batch experiments on synthetic wastewater were conducted for algal doses varying from 0.5 to 25 g/L and hydraulic retention times from 1 to 7 days. Significant removal efficiencies of greater than 90% were observed for the heavy metals, 75% of PO43- removal, and no removal of NO3- was found under continuous daylight. The single-factor ANOVA test confirms the statistical significance of the varying parameters on the pollutant removal efficiency. Langmuir and Freundlich's adsorption isotherms indicate satisfactory adsorption of the contaminants.

6. Marzan, A. Al, Hasan, M. S., Islam, M. R., Sakib, M. M., Islam, M. S., Arman, M. S., Islam, M. R., Hasnat, M. A., & Hasan, Z. (2024). Impact of betel quid on hyperglycemia among diabetes patients in Bangladesh. Journal of Advanced Biotechnology and Experimental Therapeutics, 7(3), 460–471. https://doi.org/10.5455/jabet.2024.d40

Article Metrics:
Total views: 1280, Downloads: 141
Citation Indexes: 1

Contributions:
Co-conceived the study and contributed extensively to research design. Participated in patient data collection, glycemic profiling, and betel quid usage assessment. Led statistical modeling (SPSS, Python), including logistic regression and ANOVA, to identify correlations between betel quid exposure and hyperglycemia severity. Created visualizations using R and Adobe Illustrator, interpreted findings in the context of diabetic comorbidity and regional public health trends, and contributed to drafting and reviewing the final manuscript.

Betel quid (BQ), a prevalent social habit in Asia, is often used without awareness of its harmful effects. This study explored the impact of BQ chewing on hyperglycemia among diabetic patients in northeastern Bangladesh. Specifically, this study focused on the role of areca nut, a key addictive component in BQ, in influencing hyperglycemia. Random blood glucose (RBG) tests were conducted on 961 diabetic patients, alongside lifestyle data, from August 2018 to February 2019 at Sylhet Diabetic Hospital, Bangladesh. Statistical analyses, including t-tests, Analysis of the variance (ANOVA), Fisher's exact test, and Multivariate regression, were employed to assess RBG status in BQ chewer vs. non-chewer. BQ chewers had higher RBG levels than non-chewers (263.3 ± 4.768 vs. 251.0 ± 5.915). Notably, raw areca nut users in the BQ group had significantly higher RBG levels than dry nut users (278.0 ± 8.790 vs. 252.1 ± 6.835 mg/dl), with up to 50 times more hyperglycemic effect.

7. Islam, M. A., Haque, M. A., Rahman, M. A., Hossen, F., Reza, M., Barua, A., Marzan, A. Al, Das, T., Kumar Baral, S., He, C., Ahmed, F., Bhattacharya, P., & Jakariya, M. (2022). A Review on Measures to Rejuvenate Immune System: Natural Mode of Protection Against Coronavirus Infection. Frontiers in Immunology, 13. https://doi.org/10.3389/fimmu.2022.837290

Article Metrics:

Impact Factor: 7.3

Citation Indexes: 34

Total views: 11,887, Downloads: 2,300

Contributions: Assisted in concept development through literature review. Drafted the initial manuscript, created figure illustrations using Adobe Illustrator, reviewed the manuscript, and made necessary edits.

SARS-CoV-2, a novel Corona virus strain, was first detected in Wuhan, China, in December 2019. As of December 16, 2021, almost 4,822,472 people had died and over 236,132,082 were infected with this lethal viral infection. It is believed that the human immune system is thought to play a critical role in the initial phase of infection when the viruses invade the host cells. Although some effective vaccines have already been on the market, researchers and many bio-pharmaceuticals are still working hard to develop a fully functional vaccine or more effective therapeutic agent against the COVID-19. Other efforts, in addition to functional vaccines, can help strengthen the immune system to defeat the corona virus infection. Herein, we have reviewed some of those proven measures, following which a more efficient immune system can be better prepared to fight viral infection. Among these, dietary supplements like- fresh vegetables and fruits offer a plentiful of vitamins and antioxidants.

8. Islam, M. A., Hossen, F., Rahman, M. A., Sultana, K. F., Hasan, M. N., Haque, M. A., Sosa-Hernández, J. E., Oyervides-Muñoz, M. A., Parra-Saldívar, R., Ahmed, T., Islam, M. T., Dhama, K., Sangkham, S., Bahadur, N. M., Reza, H. M., Jakariya, M., Al Marzan, A., Bhattacharya, P., Sonne, C., & Ahmed, F. (2023). An opinion on Wastewater-Based Epidemiological Monitoring (WBEM) with Clinical Diagnostic Test (CDT) for detecting high-prevalence areas of community COVID-19 infections. Current Opinion in Environmental Science & Health, 31, 100396. https://doi.org/10.1016/j.coesh.2022.100396

Article Metrics:

Impact Factor: 8.1

Citation Indexes: 36,

Captured Readers: 35, Social Media Shares, Likes & Comments: 18

Wastewater-Based Epidemiological Monitoring (WBEM) is an efficient surveillance tool during the COVID-19 pandemic as it meets all requirements of a complete monitoring system including early warning, tracking the current trend, prevalence of the disease, detection of genetic diversity as well as the up-surging SARS-CoV-2 new variants with mutations from the wastewater samples. Subsequently, Clinical Diagnostic Test (CDT) is widely acknowledged as the global gold standard method for disease monitoring, despite several drawbacks such as high diagnosis cost, reporting bias, and the difficulty of tracking asymptomatic patients (silent spreaders of the COVID-19 infection who manifest no symptoms of the disease). In this current review and opinion-based study, we first propose a combined approach for detecting COVID-19 infection in communities using wastewater and clinical sample testing, which may be feasible and effective as an emerging public health tool for the long-term nationwide surve

9. Islam, M. A., Marzan, A. Al, Bhattacharya, P., Khan, A., & Haque, M. A. (2023). Bird flu threat: An urgent call to take action to control the global spread. Journal of Infection and Public Health, 16(9), 1510–1511. https://doi.org/10.1016/j.jiph.2023.06.013

Article Metrics:

Impact Factor: 6.7

Captured Readers: 6

Citation Indexes: 4

Avian influenza virus (AIV), also known as bird flu, is a disease that affects domestic poultry, birds, and mammal species [1]. Following the COVID-19 pandemic, the highly pathogenic avian influenza (HPAI) A (H5N1) virus attracted attention as a significant new pandemic threat [2], [3]. H5N1 is enveloped, eight-segmented, -ssRNA virus, which belongs to the Orthomyxoviridae family and contains a 13.5 kb length genome, transmit from aquatic wild birds (Fig. 1). According to CDC 7,093 wild birds and 58,789,591 poultry affected by H5N1 Bird Flu. A total of 870 confirmed human-positive cases were reported between 2003 and 25 February 2023 globally in 21 countries, including 459 death cases (CFR 52.76 %) (Supplementary Table 1). Two confirmed human cases of avian influenza A H5N1 were found in Cambodia as a result of exposed infected chickens [4]. This disease is spread by birds carrying the clade 2.3.2.1c virus, but human cases had not been documented in that country since 2014.

10. Kaifa, F. H., Bhattacharya, P., Marzan, A. Al, & Islam, M. A. (2023). Tanzania - The new habitat of Marburg virus. New Microbes and New Infections, 53, 101145. https://doi.org/10.1016/j.nmni.2023.101145

Article Metrics:

Impact Factor: 4

Captured Readers: 8

Marburg virus (MARV) is a rare, virulent, and zoonotic virus causing hemorrhagic fever with a mortality rate of about 88%. Enveloped and pleomorphic morphological appearance the virus contains a negative-sense single-stranded RNA (–ssRNA). After Ebola, one of the prominent members of the family, Filoviridae is this virus under the genus Marburgvirus and species Marburg marburgvirus, which causes illness in both humans and primates other than humans [1]. The virus is comprised of seven Open Reading Fragments (ORFs) including four virion proteins (VP35, VP40, VP30, and VP24). The remaining three fragments are nucleoprotein (NP), glycoprotein (GP), and large-viral polymerase (L) [1] and each having distinct functions (Fig. 1). The Marburg virus was formerly identified in 1967 when hemorrhagic fever outbreaks concurrently emerged in labs in Belgrade, Yugoslavia (now Serbia), Marburg, Frankfurt, Germany [1]. Rousettus aegyptiacus, an African fruit bat, is the reservoir animal of the Marburg

Bacterial Genome Submission in NCBI

1. Marzan, A. A. and Islam, A., Characterization of Food Borne Pathogenic Bacteria, Bacillus cereus, NCBI Accession: OP672318.1

2. Islam, A. and Marzan, A. A., Characterization of Food Borne Pathogenic Bacteria, Kurthia gibsonii, NCBI Accession: OP672310

3. Marzan, A. A. and Islam, A., Characterization of Food Borne Pathogenic Bacteria, Bacillus amyloliquefaciens, NCBI Accession: OP660549.1

4. Marzan, A. A. and Islam, A., Characterization of Food Borne Pathogenic Bacteria, Bacillus velezensis, NCBI Accession: OP659039.1

5. Islam, A. and Marzan, A. A., Characterization of Food Borne Pathogenic Bacteria, Bacillus thuringiensis, NCBI Accession: OP659032.1

6. Islam, A. and Marzan, A. A., Characterization of Food Borne Pathogenic Bacteria, Bacillus subtilis, NCBI Accession: OP659031.1

7. Islam, A. and Marzan, A. A., Characterization of Food Borne Pathogenic Bacteria, Bacillus subtilis, NCBI Accession: OP659028.18. Islam, A. and Marzan, A. A., Characterization of Food Borne Pathogenic Bacteria, Bacillus cereus, NCBI Accession: OP659027.1

Poster Presentation

1. Exploring the Global and Temporal Selection Dynamics of HIV-1 Rev and RRE: A Computational Approach to Identifying Novel Antiviral Therapeutic Targets, International Biotechnology Conference 2025 (IBC-2025)

2. Association of variant-specific deleterious mutations of SARS-CoV-2 with immune response and opportunity for prophylactic vaccine designing. International Conference on Genomics, Nanotech, and Bioengineering-2022 (ICGNB-2022).

Abdullah Al Marzan, presenting his poster in a conference on SARS CoV-2 mutational profiling.

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