key: cord-1003004-h58644qh authors: Matin, M. Abdul; Nahid, Abdullah Al; Sarkar, Bishajit; Ullah, M. Asad; Araf, Yusha; Adnan, Nihad; Islam, Rashedul; Rahman, Mohammad Shahedur title: Genome Sequences of Two Novel Coronavirus (SARS-CoV-2) Isolates from Dhaka, Bangladesh date: 2021-07-08 journal: Microbiology resource announcements DOI: 10.1128/mra.00511-21 sha: 110a7dcca5320073b58f1285ab5d16893e837749 doc_id: 1003004 cord_uid: h58644qh This study reports the genome sequences of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in the nasopharyngeal swab specimens of two coronavirus disease 2019 (COVID-19) patients from Dhaka, Bangladesh. JU-WMSRC-Dhaka-8/2020, were found to have base pair lengths of 29,888 and 29,848, respectively, with an average coverage of over 4,313Â and 215Â, respectively. No indels were found, and the GC content was measured to be 38% for both genomes. The consensus genomes along with the related sample metadata were uploaded to the Global Initiative on Sharing All Influenza Data (GISAID) database (10) on 27 January 2021. Nextclade beta version 0.14.2 (clades.nextstrain.org) by Nextstrain (11) was utilized in the phylogenetic analysis, which assigned both sequences to SARS-CoV-2 clade 20B (Fig. 1) . The closest ancestral strains of the genomes include sequences from Bangladesh (GISAID accession no. EPI_ISL_959367, EPI_ISL_943554, and EPI_ISL_959386) and New Zealand (GISAID accession no. EPI_ISL_682280) according to Nextclade. Genome variation analysis of the consensus genomes was performed using the Genome Detective Virus Tool version 1.132 (12) , which indicated several changes in the studied genomes relative to the SARS-CoV-2 reference genome sequence of the Wuhan-Hu-1 isolate (GenBank accession no. NC_045512.2). The sequence of the hCoV-19/ Bangladesh/JU-WMSRC-Dhaka-5/2020 strain exhibited 6 synonymous and 9 nonsynonymous mutations, whereas 7 synonymous and 10 nonsynonymous mutations were observed in the sequence of the hCoV-19/Bangladesh/JU-WMSRC-Dhaka-8/2020 strain (Table 1) . Except for the Q94L mutation in the ORF7a gene, all nonsynonymous mutations were in both strains. According to the Nextstrain community build of Bangladesh (https://nextstrain.org/community/CHRF-Genomics/ncovBangladesh@main), the 9 nonsynonymous mutations common to the two studied genomes are also prevalent in other Bangladeshi SARS-CoV-2 genome sequences. However, the ORF7a Q94L mutation could not be detected in any other Bangladeshi genomes as of 4 May 2021. The most common mutations observed in SARS-CoV-2 genomes from Bangladesh include 5 nonsynonymous mutations that were also found in both studied genomes-I300F and P4715L in the ORF1ab gene, D614G in the S gene, and R203K and G204R in the N gene (13) . As more genomes of COVID-19 patients with various clinical features from various regions of the country are being sequenced on a regular basis, the evolution of the virus must be further investigated and closely monitored in order to track COVID-19 progression in Bangladesh. Data availability. The SARS-CoV-2 genome sequences from Bangladesh were deposited in the GISAID database (accession no. EPI_ISL_884087 and EPI_ISL_884088), and the raw reads have been submitted to the NCBI Sequence Read Archive (SRA). The BioProject accession no. is PRJNA701872 for both samples. The BioSample and SRA accession no. for the samples are SAMN17915311 and SAMN17915310 (BioSample) and SRR13722033 and SRR13721921 (SRA). Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. 2020. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 A pneumonia outbreak associated with a new coronavirus of probable bat origin An interactive Web-based dashboard to track COVID-19 in real time Investigating the possible origin and transmission routes of SARS-CoV-2 genomes and variants of concern in Bangladesh Novel coronavirus (2019-nCoV) nucleic acid diagnostic kit (PCR-fluorescence probing) FastQC: a quality control tool for high throughput sequence data Trimmomatic: a flexible trimmer for Illumina sequence data Fast and accurate short read alignment with Burrows-Wheeler transform Twelve years of SAMtools and BCFtools GISAID: Global Initiative on Sharing All Influenza Data: from vision to reality Nextstrain: real-time tracking of pathogen evolution Genome Detective: an automated system for virus identification from high-throughput sequencing data Global and local mutations in Bangladeshi SARS-CoV-2 genomes We thank Jahangirnagar University, Dhaka, Bangladesh, for providing the necessary funding and assistance to conduct the study.