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Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq.

ABSTRACT: Despite vaccine development and vaccination programs underway around the globe, the coronavirus disease 2019 (COVID-19) pandemic has not been controlled as the SARS-CoV-2 virus is evolving and new variants are emerging. This study was conducted to sequence and molecularly characterize the representing samples from the early fourth SARS-CoV-2 wave in Iraq. Here, we have performed next-generation sequencing of whole-genome sequencing of two representing samples from the country's early beginning of the fourth pandemic wave. The samples were sequenced using Illumina Miseq system, and the reference sequences were retrieved from GISAID database. Phylogenetic analysis was performed through Mega software. This study provides an initial sequence analysis and molecular characterization of the first Omicron variant cases recorded in the country. Our analysis revealed many mutations on the spike glycoprotein, especially on the receptor binding domain, with potential impact on immune escape and infectivity. The study findings suggest considering the highly mutated immunogenic epitope of the Omicron variant as a reference for developing a new vaccine for combating the ongoing pandemic.

SUBMITTER: Ahmed JQ

PROVIDER: S-EPMC9359486 | biostudies-literature | 2022 Sep-Oct

REPOSITORIES: biostudies-literature

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Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq.

Ahmed Jivan Qasim JQ Maulud Sazan Qader SQ Al-Qadi Rawand R Mohamed Teroj Abdulrahman TA Tayib Gahin Abdulraheem GA Hassan Akheenk Mustafa AM Taha Luqman Saleh LS Qasim Khairi Mohammed KM Tawfeeq Mohammed Abid MA

The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases 20220808 5

Despite vaccine development and vaccination programs underway around the globe, the coronavirus disease 2019 (COVID-19) pandemic has not been controlled as the SARS-CoV-2 virus is evolving and new variants are emerging. This study was conducted to sequence and molecularly characterize the representing samples from the early fourth SARS-CoV-2 wave in Iraq. Here, we have performed next-generation sequencing of whole-genome sequencing of two representing samples from the country's early beginning o ...[more]

PMID: 35970304

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Project description:ObjectivesThe aim of this study was to first assess the knowledge and perception of first-year university students in Iraq about COVID-19 in general and SARS-CoV-2 latest variant of concern, and to evaluate the attitudes towards protection measures including vaccination.Study designA cross-sectional study was conducted among newly enrolled students at the American University of Iraq-Baghdad. Mann-Whitney U and Kruskal-Wallis tests were used to test an association between the outcomes measured on a 5-point Likert scale and the binary and the categorical independent variables, respectively. χ2 test was used to test the association between nominal categorical variables, while Kendall's τ-b was used for ordinal variables.ParticipantsStudents (n=432) were invited to fill out a survey specifically tailored to assess their knowledge, perception and attitude towards Omicron variant and COVID-19 vaccines acceptance. 363 students enrolled in various majors participated in this study.ResultsAssessment of COVID-19 knowledge and perception revealed that students still lack reliable info and data about FDA-approved treatment options (70.5%), SARS-CoV-2 variants (96.5%) and approved vaccines. Students' attitude and practices towards recommended safety measures should be reassessed to better manage the pandemic. Adherence level was shown to be associated with the belief in its capacity to effectively manage the new variant. Interestingly, 85% of the students have received at least one dose of approved vaccine. A significant positive correlation was detected between the level of adherence to recommended precautions and the intention to take a third booster shot if proven effective.ConclusionsStudents' reliable knowledge about COVID-19 pandemic including the various strains and approved vaccines should be improved to better manage the pandemic and set foundations for a more appropriate approach when another pandemic occurs. Special workshops should be organised to ensure that students and the public have a more trusted source of information about COVID-19.

Project description:Genomic epidemiology of SARS-CoV-2 is imperative to explore the transmission, evolution, and also pathogenicity of viruses. The emergence of SARS-CoV-2 variants of concern posed a severe threat to the global public health efforts. To assess the potential consequence of these emerging variants on public health, continuous molecular epidemiology is of vital importance. The current study has been designed to investigate the major SARS-CoV-2 variants and emerging mutations in virus structural and non-structural proteins (NSP) during the fourth wave in September 2021 from the Punjab province of Pakistan. Twenty SARS-CoV-2 positive samples have been collected from major cities were subjected to next-generation sequencing. Among the 20 whole genomes (GenBank Accession SRR16294858-SRR16294877), 2 samples failed to be completely sequenced. These genome sequences harbored 207 non-synonymous mutations, among which 19 were unique to GISAID. The genome sequences were detected: Delta 21I, 21J variants (B.1.617.2). Mutation's spike_F157del, spike_P681R, spike_T478K, spike_T19R, spike_L452R, spike_D614G, spike_G142D, spike_E156G, and spike_R158del have been detected in all samples where K1086Q, E554K, and C1250W were unique in spike protein. These genomic sequences also harbored 129 non-synonymous mutations in NSP. The most common were NSP3_P1469S (N = 17), NSP3_A488S (N = 17), NSP3_P1228L (N = 17), NSP4_V167L (N = 17), NSP4_T492I (N = 17), NSP6_T77A (N = 17), NSP14_A394V (N = 17), NSP12_G671S (N = 18), and NSP13_P77L (N = 18). The mutation, F313Y in NSP12, detected in the current study, was found in a single isolate from Belgium. Numerous other unique mutations have been detected in the virus papain-like protease (NSP3), main protease (NSP5), and RNA-dependent RNA polymerase (NSP12). The most common non-synonymous mutations in the spike protein were subjected to stability analysis, exhibiting a stabilizing effect on structures. The presence of Delta variants may affect therapeutic efforts and vaccine efficacy. Continuous genomic epidemiology of SARS-CoV-2 in Pakistan may be useful for better management of SARS-CoV-2 infections.

Dataset Information

Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq.

Publications

Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq.

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