Dataset Information

Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq.

ABSTRACT: The coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an Iraqi patient was sequenced for the first-time using Illumina MiSeq technology. There was a D614G mutation in the spike protein-coding sequence. This report is valuable for better understanding the spread of the virus in Iraq.

SUBMITTER: Al-Rashedi NAM

PROVIDER: S-EPMC7844075 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq.

Al-Rashedi Nihad A M NAM Licastro Danilo D Rajasekharan Sreejith S Dal Monego Simeone S Marcello Alessandro A Munahi Murad G MG Odda Basel Saber BS Alabdali Yasir Adil Jabbar YAJ ALObaidi Laith A H LAH Jasim Ali A Abdulzahra Ibrahem A IA Kadhim Karar K Awad Ali A Bachay Mohamed M

Microbiology resource announcements 20210128 4

The coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an Iraqi patient was sequenced for the first-time using Illumina MiSeq technology. There was a D614G mutation in the spike protein-coding sequence. This report is valuable for better understanding the spread of the virus in Iraq. ...[more]

PMID: 33509990

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Project description:A new human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged at the end of 2019 in Wuhan, China that caused a range of disease severities; including fever, shortness of breath, and coughing. This disease, now known as coronavirus disease 2019 (COVID-19), quickly spread throughout the world, and was declared a pandemic by the World Health Organization in March of 2020. As the disease continues to spread, providing rapid characterization has proven crucial to better inform the design and execution of control measures, such as decontamination methods, diagnostic tests, antiviral drugs, and prophylactic vaccines for long-term control. Our work at the United States Army's Combat Capabilities Development Command Chemical Biological Center (DEVCOM CBC) is focused on engineering workflows to efficiently identify, characterize, and evaluate the threat level of any potential biological threat in the field and more remote, lower resource settings, such as forward operating bases. While we have successfully established untargeted sequencing approaches for detection of pathogens for rapid identification, our current work entails a more in-depth sequencing analysis for use in evolutionary monitoring. We are developing and validating a SARS-CoV-2 nanopore sequencing assay, based on the ARTIC protocol. The standard ARTIC, Illumina, and nanopore sequencing protocols for SARS-CoV-2 are elaborate and time consuming. The new protocol integrates Oxford Nanopore Technology's Rapid Sequencing Kit following targeted RT-PCR of RNA extracted from human clinical specimens. This approach decreases sample manipulations and preparation times. Our current bioinformatics pipeline utilizes Centrifuge as the classifier for quick identification of SARS-CoV-2 and RAMPART software for verification and mapping of reads to the full SARS-CoV-2 genome. ARTIC rapid sequencing results, of previous RT-PCR confirmed patient samples, showed that the modified protocol produces high quality data, with up to 98.9% genome coverage at >1,000x depth for samples with presumably higher viral loads. Furthermore, whole genome assembly and subsequent mutational analysis of six of these sequences identified existing and unique mutations to this cluster, including three in the Spike protein: V308L, P521R, and D614G. This work suggests that an accessible, portable, and relatively fast sample-to-sequence process to characterize viral outbreaks is feasible and effective.

Dataset Information

Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq.

Publications

Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq.

Similar Datasets

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