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Woldemariam KY, Yuan J, Wan Z, Yu Q, Cao Y, Mao H, Liu Y, Wang J, Li H, Sun B. Celiac Disease and Immunogenic Wheat Gluten Peptides and the Association of Gliadin Peptides with HLA DQ2 and HLA DQ8. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2021.1907755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Kalekristos Yohannes Woldemariam
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Juanli Yuan
- School of Pharmacy, Nanchang University, Nanchang, China
| | - Zhen Wan
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Qinglin Yu
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Yating Cao
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Huijia Mao
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Yingli Liu
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Jing Wang
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Hongyan Li
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
| | - Baoguo Sun
- School of Food and Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, China
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Islam MR, Hoque MN, Rahman MS, Alam ASMRU, Akther M, Puspo JA, Akter S, Sultana M, Crandall KA, Hossain MA. Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity. Sci Rep 2020; 10:14004. [PMID: 32814791 PMCID: PMC7438523 DOI: 10.1038/s41598-020-70812-6] [Citation(s) in RCA: 195] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/08/2020] [Indexed: 01/17/2023] Open
Abstract
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.
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Affiliation(s)
- M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Masuda Akther
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - J Akter Puspo
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Salma Akter
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, USA
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
- Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
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Computational screening of potential non-immunoglobulin scaffolds using overlapped conserved residues (OCR)-based fingerprints. KOREAN J CHEM ENG 2018. [DOI: 10.1007/s11814-017-0350-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Identification of novel cytochrome P450 homologs using overlapped conserved residues based approach. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-015-0013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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