key: cord-0741827-a4f4au45
authors: Adnan, Nihad; Khondoker, Mohib Ullah; Rahman, M. Shaminur; Ahmed, M. Firoz; Sharmin, Shahana; Sharif, Nadim; Azmuda, Nafisa; Akter, Salma; Nahar, Shamsun; Mou, Taslin Jahan; Marzan, Mahfuza; Liza, Syeda Moriam; Jahan, Nowshin; Ali, Tamanna; Khandker, Shahad Saif; Jamiruddin, Maha; Chaity, Mousumi Akter; Caller, Laura Grace; Haq, M. Ahsanul; Jamiruddin, Mohd Raeed
title: Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh
date: 2021-03-11
journal: Microbiol Resour Announc
DOI: 10.1128/mra.00124-21
sha: 6bd978f5aa48fc87446848e74a52f50ad9dc958d
doc_id: 741827
cord_uid: a4f4au45

Here, we report the coding-complete genome sequences of nine clinical severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and their mutations. The samples were collected from nine Bangladeshi coronavirus disease 2019 (COVID-19) patients. We have identified the E484K escape mutation and the S359T mutation within the spike protein coding region of the sequenced genomes.

The novel mutations were confirmed with the EpiCov tool, integrated in the Global Initiative on Sharing All Influenza Data (GISAID) database (7) . All mutations and deletions were confirmed by area-wise coverage using Snippy (5) .

Eight strains (GRBL_S1, GRBL_S2, GRBL_S3, GRBL_S4, GRBL_S6, GRBL_S9, GRBL_S10, and GRBL_S14) belong to the emerging clade 20B, whereas one strain (GRBL_S11) is affiliated with the 20F clade (Table 1 ). In this announcement, among the multitude of mutations, we are reporting two mutations, one at position 1450 from G (0 evidence) to A (267 evidence) in GRBL_S1, which results in the amino acid substitution of E484K, and one at position 1076 from G (0 evidence) to C (4,559 evidence) in GRBL_S9, which results in S359T in the spike protein region ("evidence" relates to area-wise coverage obtained by Snippy tools for short-read sequences generated by Illumina MiniSeq). The former mutation was reported in the South African variant as an escape mutation (8, 9) . The E484K substitution was observed in a cluster containing D614G, P681H, and S13I changes (GRBL_S1), while the S359T amino acid substitution was observed in a cluster containing D614G and A942V changes (GRBL_S9). Additionally, we found cluster substitutions D614G, Q677H, and A871V in the spike protein of GRBL_S10. Within the open reading frame 1ab (ORF1ab) region, we observed amino acid substitutions of I1257S in GRBL_S1 and L151I and T275A in GRBL_S14. The complete list of amino acid substitutions is provided in Fig. 1 .

It is also noteworthy that in two samples, GRBL_S2 (2,446 evidence) and GRBL_S3 (68 evidence), the deletion of GATCAT and its subsequent replacement by G at nucleotide position 108 of ORF7b resulted in the introduction of a stop codon, ultimately resulting in a frameshift mutation and D36E substitution, potentially without any loss of function (10) . The patients harboring these variants were detected as family members residing within the same household. Substitutions pertaining to the nucleocapsid protein coding region were S327L, G18V, and A252S in samples GRBL_S1, GRBL_S11, and GRBL_S14, respectively. Further investigations are required to identify the effects of the substitutions on the outcomes of coronavirus disease 2019 (COVID-19). CoV-2 genomes were submitted  to the GISAID database under the identifiers EPI_ISL_774976, EPI_ISL_775019,  EPI_ISL_775020, EPI_ISL_890189, EPI_ISL_775215, EPI_ISL_775218, EPI_ISL_890192,  EPI_ISL_890193, and EPI_ISL_890194 and to the NCBI GenBank under the accession  numbers MW532093, MW532094, MW532095, MW532096, MW532097, MW532098 , MW532099, MW532100, and MW532101 ( Table 1) . The raw reads were submitted to the NCBI SRA under BioProject accession number PRJNA692653 and SRA accession number SRP302071.

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