Materials and Methods
The Global Initiative on Sharing Avian Influenza Data (GISAID) was founded in 2006, and, since 2010, has been hosted by the German Federal Ministry of Food, Agriculture and Consumer Protection. GISAID has also become a coronavirus repository since December 2019. As of 13 May 2020, the cutoff point for our phylogenetic analysis, the GISAID database (https://www.gisaid.org/) had compiled 16,667 coronavirus full genomes, isolated from humans, Chinese pangolins, and batRhinolophus affinis . Among the all deposited genome sequences 1485 from all Asian countries. Although SARS-CoV-2 is an RNA virus, the deposited sequences, by convention, are in DNA format. We discarded partial sequences, and used only the most complete genomes that we aligned to the full reference genome (NC_045512.2) by Wu et al. (2020) [5] comprising 29,903 nucleotides which was retried from NCBI (https://www.ncbi.nlm.nih.gov/nuccore). Finally, to ensure comparability, we truncated the flanks of all sequences to the consensus range 56 to 29,797, with nucleotide position numbering according to the Wuhan 1 reference sequence [5]. To analyze the obtained 1st Bangladeshi SARS-CoV-2 genome derived from the infected female patients aged 22 (GISAID accession ID: EPI_ISL_437912) which was submitted by Child Health Research Lab, Bangladesh in a phylogenetic context, a dataset of 32 available SARS-Cov-2 complete genomes from different Asian countries followed by few other continent countries was retrieved from GISAID (https://www.gisaid.org/, last access 12 May 2020). At least one sequence from all Asian countries who has submitted SARS-Cov-2 genome in the GISAID database was taken to reveal the draft scenario of the circulating SARS-CoV-2 strain in this Asia zone in comparison of newly revealed Genome from Bangladesh. Sequence alignment was performed using Multiple Sequence Comparison by Log- Expectation (MUSCLE) software (http://www.clustal.org)[6]. Estimation of the best fitting substitution model (Hasegawa, Kishino, and Yano, HKY model) and inference of the phylogenetic tree were conducted by a neighbor-joining approach using Molecular Evolutionary Genetics Analysis across Computing Platforms (MEGA 7; https://www.megasoftware.net/) [7]. Support for the tree topology was estimated with 1,000 bootstrap replicates. Using an alignment, the single nucleotide polymorphisms (SNPs) composition and the potentially resulting variable amino-acids in derived protein sequences compared with the Wuhan reference sequences (NC_045512), were further investigated with six other genome sequences (EPI_ISL_430111, EPI_ISL_437762, EPI_ISL_412974, EPI_ISL_417444, EPI_ISL_427813, EPI_ISL_437438) that clustered or non-clustered from Asia and Europe with the sequence of the patient in Bangladesh. For mutation type analysis MEGA7 and Datamonkey.org web server was used [8]. For analysis of the novel mutation NCBI Blast was used (https://blast.ncbi.nlm.nih.gov/Blast.cgi). Protein structures were predicted using Phyre2 (Protein homology/analogy recognition engine v2.0) [9] and I-TASSER (Iterative threading assembly refinement) [10]. Templates with the highest confidence were used to generate the model in each case. For Phyre2, intense model was used. Generated PDB files were analysed and aligned using PyMOL v2.3.2. Images were processed in adobe illustrator vCS6. Secondary structures were predicted using PSIPRED included in Phyre2.