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Genome sequence analysis of SARS-COV-2 isolated from a COVID-19 patient in Erbil, Iraq.

ABSTRACT: In the city of Wuhan, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first recognized among humans at the end of December 2019, and has since spread to every country around the world. The emergence of this new coronavirus has attracted global attention to work towards finding a treatment and developing an effective vaccine against the virus. In this study, we sequence a full genome of SARS-COV-2 isolated from a male patient in the city of Erbil, Iraq. The virus was sequenced using Sanger sequencer and 21 distinct mutations were found in our isolate compared to the full genome sequence of the SARS-COV-2 isolated from the city of Wuhan/China (Accession number: NC_045512.2). Sequence analysis showed that four of the mutations were located at the spike glycoprotein (S), and ten of them were in nonstructural proteins (nsp1, nsp3, nsp12, and orf3a), which had been shown to be related to structural changes at various sites. Moreover, phylogenetic analysis and transmission supported the conclusion that the cases in Iraq were of independent origins of infections and had a close relation to the isolates from Iran. This is the first report on the DNA sequence of the SARS-CoV-2 genome isolated from the Kurdistan region of Iraq.

SUBMITTER: Hussen BM

PROVIDER: S-EPMC8818371 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundCoronaviruses are a group of viruses that belong to the Family Coronaviridae, genus Betacoronavirus. In December 2019, a new coronavirus disease (COVID-19) characterized by severe respiratory symptoms was discovered. The causative pathogen was a novel coronavirus known as 2019-nCoV and later as SARS-CoV-2. Within two months of its discovery, COVID-19 became a pandemic causing widespread morbidity and mortality.MethodologyWhole genome sequence data of SARS-CoV-2 isolated from Nigerian COVID-19 cases were retrieved by downloading from GISAID database. A total of 18 sequences that satisfied quality assurance (length ≥29,700 nts and number of unknown bases denoted as "N" ≤ 5%) were used for the study. In addition, genome sequence of SARS-CoV-2 obtained from Nigeria's COVID-19 index case (Accession ID: EPI_ISL_413550) and the reference genome (Accession NC_ 045512.2) were obtained from GISAID and the GenBank databases, respectively. Multiple sequence alignment (MSA) was done in MAFFT (Version 7.471) while SNP calling was implemented in DnaSP (Version 6.12.03), respectively and then visualized in Jalview (Version 2.11.1.0). Phylogenetic analysis was with MEGA X software.ResultsNigerian SARS-CoV-2 had 99.9% genomic similarity with four large conserved genomic regions. A total of 66 SNPs were identified out of which 31 were informative. Nucleotide diversity assessment gave Pi = 0.00048 and average SNP frequency of 2.22 SNPs per 1000 nts. Non-coding genomic regions particularly 5'UTR and 3'UTR had a SNP density of 3.77 and 35.4, respectively. The region with the highest SNP density was ORF10 with a frequency of 8.55 SNPs/1000 nts). This value was significantly higher (P < 0.01) than that of the spike gene, the region of greatest interest in SARS-CoV-2 genomics. Majority (72.2%) of viruses in Nigeria are of L lineage with preponderance of D614G mutation which accounted for 11 (61.1%) out of the 18 viral sequences. Nigeria SARS-CoV-2 revealed 3 major clades namely Oyo, Ekiti and Osun on a maximum likelihood phylogenetic tree.Conclusion and recommendationThere was a preponderance of L lineage (to include the new lineage scheme) and D614G mutants. Nigerian SARS-CoV-2 genome revealed ORF1ab as the region containing the highest SNP density as compared to the spike gene. The implication of this distribution of SNPs for the empirical lower infectivity of SARS-CoV-2 in Nigeria is discussed. This also underscores the need for more aggressive testing and treatment of COVID-19 in Nigeria. Additionally, attempt to produce testing kits for COVID-19 in Nigeria should consider the conserved regions identified in this study. Strict adherence to COVID-19 preventive measure is recommended in view of Nigerian SARS-CoV-2 phylogenetic clustering pattern, which suggests intensive community transmission possibly rooted in communal culture characteristic of many ethnicities in Nigeria.

Project description:BackgroundTransmission within families and multiple spike protein mutations have been associated with the rapid transmission of SARS-CoV-2. We aimed to: (1) describe full genome characterization of SARS-CoV-2 and correlate the sequences with epidemiological data within family clusters, and (2) conduct phylogenetic analysis of all samples from Yogyakarta and Central Java, Indonesia and other countries.MethodsThe study involved 17 patients with COVID-19, including two family clusters. We determined the full-genome sequences of SARS-CoV-2 using the Illumina MiSeq next-generation sequencer. Phylogenetic analysis was performed using a dataset of 142 full-genomes of SARS-CoV-2 from different regions.ResultsNinety-four SNPs were detected throughout the open reading frame (ORF) of SARS-CoV-2 samples with 58% (54/94) of the nucleic acid changes resulting in amino acid mutations. About 94% (16/17) of the virus samples showed D614G on spike protein and 56% of these (9/16) showed other various amino acid mutations on this protein, including L5F, V83L, V213A, W258R, Q677H, and N811I. The virus samples from family cluster-1 (n = 3) belong to the same clade GH, in which two were collected from deceased patients, and the other from the survived patient. All samples from this family cluster revealed a combination of spike protein mutations of D614G and V213A. Virus samples from family cluster-2 (n = 3) also belonged to the clade GH and showed other spike protein mutations of L5F alongside the D614G mutation.ConclusionsOur study is the first comprehensive report associating the full-genome sequences of SARS-CoV-2 with the epidemiological data within family clusters. Phylogenetic analysis revealed that the three viruses from family cluster-1 formed a monophyletic group, whereas viruses from family cluster-2 formed a polyphyletic group indicating there is the possibility of different sources of infection. This study highlights how the same spike protein mutations among members of the same family might show different disease outcomes.

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Genome sequence analysis of SARS-COV-2 isolated from a COVID-19 patient in Erbil, Iraq.

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