key: cord-0718359-udgn0he9
authors: Kim, Minwoo; Lee, Youn-Jung; Yoon, Jae Sun; Ahn, Jin Young; Kim, Jung Ho; Choi, Jun Yong; Oh, Jong-Won
title: Genome Sequences of Two GH Clade SARS-CoV-2 Strains Isolated from Patients with COVID-19 in South Korea
date: 2021-01-07
journal: Microbiol Resour Announc
DOI: 10.1128/mra.01384-20
sha: da8f32a7906e166d5884f4b6b291c77ad99f10ed
doc_id: 718359
cord_uid: udgn0he9

We report the genome sequences of two GH clade severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains isolated from nasopharyngeal swabs from patients with coronavirus disease 2019 (COVID-19) in South Korea. These strains had two mutations in the untranslated regions and seven nonsynonymous substitutions in open reading frames, compared with Wuhan/Hu-1/2019, showing 99.96% sequence identity.

nucleotides from their 59 and 39 ends [excluding the poly(A) tail], respectively (99.85% horizontal coverage), were 99.96% identical to the reference sequence. They both have a genomic GC content of 38%. Phylogenetic analysis revealed that these two isolates belong to the GH clade, which is currently most prevalent worldwide (9, 10) , according to the GISAID classification (11) (Fig. 1 ). There were a total of 6 and 7 amino acid substitutions for YS006 and YS008, respectively, in comparison to the reference strain (Table 1) . Both strains had C-to-T and G-to-T nucleotide changes in the 59 untranslated region (UTR) and the 39 UTR, respectively. A unique S6L substitution in the envelope (E) protein differentiated the YS008 strain from the YS006 and Wuhan/Hu-1/2019 strains. FIG 1 Phylogenetic tree of the genome sequences of SARS-CoV-2/human/KOR/YS006/2020 and SARS-CoV-2/human/KOR/YS008/2020, along with 58 other randomly chosen sequences, including 30 sequences of South Korean isolates of SARS-CoV-2 retrieved from Nextstrain (nextstrain.org). Multiple sequence alignments were conducted with MUSCLE v3.8.31 (12) , and the phylogenetic tree was constructed using the Molecular Evolutionary Genetics Analysis (MEGA) v7.0 software by the neighbor-joining method with 1,000 bootstrap replicates (13) . Shown in parentheses after the strain name and GISAID accession number are the clade to which it belongs and the collection date (month-day) for each strain. The sequences reported in this announcement are shown in bold. The SARS-CoV-2 isolates are presented in seven different colors for the different clades (shown in the key), classified according to GISAID classification. The scale bar represents the number of nucleotide substitutions per site.

Data availability. The sequences of SARS-CoV-2/human/KOR/YS006/2020 and SARS-CoV-2/human/KOR/YS008/2020 were deposited in the NCBI database (GenBank accession numbers MW345824 and MW345825, respectively) and in the GISAID database (https://www.gisaid.org) (accession numbers EPI_ISL_660109 and EPI_ISL_660110, respectively). The raw reads for the YS006 and YS008 strains were deposited in the NCBI Sequence Read Archive (SRA) database (accession numbers SRR13153716 and SRR13153715, respectively). Gene name b Amino acid change c Hu-1 (L) a YS006 (GH) YS008 (GH)  241  C  T  T  59 UTR  1059  C  T  T  nsp2  T85I  3037  C  T  T  nsp3  11916  C  T  T  nsp7  S25L  14408  C  T  T  nsp12  P323L  16650  C  T  T  nsp13  20675  A  T  T  nsp16  Q6L  23403 A 

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