Abdullah Al Marzan
@sust.edu
Department of Biochemistry and Molecular Biology
Shahjalal University of Science and Technology
Abdullah Al Marzan completed some data science and programming languages courses and participated in programming contests, including the "Rosalind Programming Contest". He worked under a nonprofitable organization, "KIN,"-built to develop unprivileged children for one year. He also works under a research institute, "Red Green Research Institute, "-a nonprofitable organization, and performs some training programs as a trainer.
And now, he is working to utilize his experience and knowledge regarding molecular biology, data science and programming languages to the betterment of the disease outbreak scenario in the world.
EDUCATION
Abdullah Al Marzan completed his master's program in Biochemistry and Molecular Biology department, SUST and is currently a research assistant. He had worked on several projects including but not limited to wastewater management systems, SARS-Cov-2, non-communicable diseases and blue-green algae development.
RESEARCH, TEACHING, or OTHER INTERESTS
Biochemistry, Genetics and Molecular Biology, Computational Theory and Mathematics, Atomic and Molecular Physics, and Optics, Chemistry
Scopus Publications
Scholar Citations
Scholar h-index
Scholar i10-index
Scopus Publications
Md. Aminul Islam, Abdullah Al Marzan, Md. Sakil Arman, Shatila Shahi, Tahsin Islam Sakif, Maqsud Hossain, Tofazzal Islam, and M. Nazmul Hoque
Springer Science and Business Media LLC
AbstractThe 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. The ‘G’ clade was dominant in the SARS-CoV-2 genomes of Asian, African, and North American regions, while the ‘GRY’ clade prevailed in Europe. In our analysis, we identified 35,799 nucleotide (NT) mutations throughout the genome, with the highest frequency (11,402 occurrences) found in the spike protein. Notably, we observed 4150 point-specific amino acid (AA) mutations in SARS-CoV-2 genomes, with D614G (20%) and N501Y (14%) identified as the top two deleterious mutations in the spike protein on a global scale. Furthermore, we detected five common deleterious AA mutations, including G18V, W45S, I33T, P30L, and Q418H, which play a key role in defining each clade of SARS-CoV-2. Our novel findings hold potential value for genomic surveillance, enabling the monitoring of the evolving pattern of SARS-CoV-2 infection, its emerging variants, and their impact on the development of effective vaccination and control strategies.
Md Aminul Islam, Abdullah Al Marzan, Prosun Bhattacharya, Ahrar Khan, and Md Atiqul Haque
Elsevier BV
Fatema Hasan Kaifa, Prosun Bhattacharya, Abdullah Al Marzan, and Md Aminul Islam
Elsevier BV
Md. Aminul Islam, Shatila Shahi, Abdullah Al Marzan, Mohammad Ruhul Amin, Mohammad Nayeem Hasan, M. Nazmul Hoque, Ajit Ghosh, Abanti Barua, Abbas Khan, Kuldeep Dhama,et al.
Frontiers Media SA
Introduction: Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had a disastrous effect worldwide during the previous three years due to widespread infections with SARS-CoV-2 and its emerging variations. More than 674 million confirmed cases and over 6.7 million deaths have been attributed to successive waves of SARS-CoV-2 infections as of 29th January 2023. Similar to other RNA viruses, SARS-CoV-2 is more susceptible to genetic evolution and spontaneous mutations over time, resulting in the continual emergence of variants with distinct characteristics. Spontaneous mutations of SARS-CoV-2 variants increase its transmissibility, virulence, and disease severity and diminish the efficacy of therapeutics and vaccines, resulting in vaccine-breakthrough infections and re-infection, leading to high mortality and morbidity rates.Materials and methods: In this study, we evaluated 10,531 whole genome sequences of all reported variants globally through a computational approach to assess the spread and emergence of the mutations in the SARS-CoV-2 genome. The available data sources of NextCladeCLI 2.3.0 (https://clades.nextstrain.org/) and NextStrain (https://nextstrain.org/) were searched for tracking SARS-CoV-2 mutations, analysed using the PROVEAN, Polyphen-2, and Predict SNP mutational analysis tools and validated by Machine Learning models.Result: 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 analysis protruding that Omicron is more transmissible.Discussion: The pathogenesis of the Omicron variant could be prevented if the deleterious and persistent unique immunosuppressive mutations can be targeted for vaccination or small-molecule inhibitor designing. Thus, our findings will help researchers monitor and track the continuously evolving nature of SARS-CoV-2 strains, the associated genetic variants, and their implications for developing effective control and prophylaxis strategies.
Md. Aminul Islam, Foysal Hossen, Md. Arifur Rahman, Khandokar Fahmida Sultana, Mohammad Nayeem Hasan, Md. Atiqul Haque, Juan Eduardo Sosa-Hernández, Mariel Araceli Oyervides-Muñoz, Roberto Parra-Saldívar, Tanvir Ahmed,et al.
Elsevier BV
Md. Jakariya, Firoz Ahmed, Md. Aminul Islam, Abdullah Al Marzan, Mohammad Nayeem Hasan, Maqsud Hossain, Tanvir Ahmed, Ahmed Hossain, Hasan Mahmud Reza, Foysal Hossen,et al.
Elsevier BV
Md. Aminul Islam, Md. Atiqul Haque, Md. Arifur Rahman, Foysal Hossen, Mahin Reza, Abanti Barua, Abdullah Al Marzan, Tuhin Das, Sumit Kumar Baral, Cheng He,et al.
Frontiers Media SA
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, enabling to build of a healthy immune system. While the pharmacologically active components of medicinal plants directly aid in fighting against viral infection, supplementary supplements combined with a healthy diet will assist to regulate the immune system and will prevent viral infection. In addition, some personal habits, like- regular physical exercise, intermittent fasting, and adequate sleep, had also been proven to aid the immune system in becoming an efficient one. Maintaining each of these will strengthen the immune system, allowing innate immunity to become a more defensive and active antagonistic mechanism against corona-virus infection. However, because dietary treatments take longer to produce beneficial effects in adaptive maturation, personalized nutrition cannot be expected to have an immediate impact on the global outbreak.