key: cord-0865944-ffxo3tz2
authors: Alemayehu, Dawit Hailu; Adnew, Bethlehem; Alemu, Fekadu; Tefera, Dessalegn Abeje; Seyoum, Tamrayehu; Beyene, Getachew Tesfaye; Gelanew, Tesfaye; Negash, Abel Abera; Abebe, Markos; Mihret, Adane; Bayih, Abebe Genetu; Abdissa, Alemseged; Mulu, Andargachew
title: Whole-Genome Sequences of SARS-CoV-2 Isolates from Ethiopian Patients
date: 2021-09-23
journal: Microbiol Resour Announc
DOI: 10.1128/mra.00721-21
sha: aacc280279302585444fc614ae5aaa0b14eda714
doc_id: 865944
cord_uid: ffxo3tz2

Three complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Ethiopian patients were compared with deposited global genomes. Two genomes belonged to genetic group 20A/B.1/GH, and the other belonged to genetic group 20A/B.1.480/GH. Enhancing genomic capacity is important to investigate the transmission and to monitor the evolution and mutational patterns of SARS-CoV-2 in this country.

Nextclade v0.13.0 was also implemented for clade assignment and variant annotation. The phylogenetic tree was generated with Nextstrain/Augur using its default subsampling scheme and focusing on country Ethiopia, region Africa, where 1,960 samples were subsampled between December 2019 and February 2021; the tree was visualized using the Nextstrain/Auspice tool. Lineage assignments were made using the Phylogenetic Assignment of Named Global Outbreak Lineages (Pangolin) v1.07 tool (https://github.com/hCoV-2019/ pangolin) and clades from GISAID (https://www.gisaid.org). All tools were run with default parameters unless otherwise specified. There is 99.68 to 99.92% sequence identity using BLAST between the full genome sequences of the isolates and the reference strain at the nucleotide level and 99.94% identity at the amino acid level. All three isolates have 99.97 to 100% coverage, with 100% coverage of the coding region. The genome sizes were 29,860, 29,856, and 29,871 bp, with GC contents of 53%, 51%, and 49%, for isolates MZ172407, MZ172408, and MZ172409, respectively. Similarly, the average coverage depths were 2,56.7Â (range, 1Â to 3,183Â), 23.8Â (range, 1Â to 1,110Â), and 1,288.3Â (range, 4Â to 8,002Â) for the isolates MZ172407, MZ172408, and MZ172409, respectively.

Phylogenomic analysis showed that two of the detected SARS-CoV-2 isolates (isolates MZ172408 and MZ172409) belonged to lineage B.1 of the Pangolin lineage, sharing the most common recent ancestor with viruses detected in Germany (Fig. 1) . One of the isolates (isolate MZ172407) was found to belong to lineage B.1.480. According to Nextstrain (10), the phylogenetic tree revealed that all of the isolates belonged to Nextstrain clade 20A and GISAID clade GH.

Mutations among the three SARS-CoV-2 strains were identified throughout the whole genome, with reference to the SARS-CoV-2 Wuhan strain (GenBank accession number NC_045512.2), and marked nucleotide differences in some positions were found, as shown in Table 1 . In general, several synonymous and nonsynonymous mutations with Variants were called using Snippy (https://github.com/tseemann/snippy) and Nextclade.

b pyrimidine exchanges (C to T or T to C) (55%) were observed in all three genomes (Table 1) . Currently, we are sequencing more genomes to further investigate the transmission and to monitor the evolution and mutational patterns of SARS-CoV-2 in this country. Data availability. The coding-complete sequences were deposited in GenBank with accession numbers MZ172407, MZ172408, and MZ172409 and SRA accession numbers SAMN20692030, SAMN20692031, and SAMN20692032 and in GISAID (https:// www.gisaid.org) with accession numbers EPI_ISL_2970353, EPI_ISL_2970354, and EPI_ISL_2970355 for Ethiopia/AHRI-01/2020, Ethiopia/AHRI-02/2020, and Ethiopia/ AHRI-03/2020, respectively.

A new coronavirus associated with human respiratory disease in China

Genetic diversity of SARS-CoV-2 over a oneyear period of the COVID-19 pandemic: a global perspective

Comprehensive workflow for detecting coronavirus using Illumina benchtop systems. Illumina

FastQC: a quality control tool for high throughput sequence data

Trimmomatic: a flexible trimmer for Illumina sequence data

Improved metagenomic analysis with Kraken 2

Fast gapped-read alignment with Bowtie 2

The Sequence Alignment/Map format and SAMtools

Fast and accurate short read alignment with Burrows-Wheeler transform

Nextstrain: real-time tracking of pathogen evolution

This work was supported by the Federal Ministry of Health and the Armauer Hansen Research Institute core fund from SIDA and NORAD.