About: Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic

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About: Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic
Creator	Giovanetti, Marta Fonseca, Vagner Affiliations, Brazil, De Oliveira, Tulio Horizonte, Belo Carols Alcantara, Luiz Chimukangara, Benjamin Fish, Maryam Gazy, Inbal Giandhari, Jennifer Khanyile, Khulekani Lessells, Richard Moosa, Yunus Pillay, Sureshnee Singh, Lavanya Tegally, Houriiyah Wilkinson, Eduan Gerais, Minas
Source	BioRxiv
abstract	The COVID-19 pandemic spread very fast around the world. A few days after the first detected case in South Africa, an infection started a large hospital outbreak in Durban, KwaZulu-Natal. Phylogenetic analysis of SARS-CoV-2 genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. In this manuscript, we outline the obstacles we encountered in order to genotype SARS-CoV-2 in real-time during an urgent outbreak investigation. In this process, we encountered problems with the length of the original genotyping protocol, reagent stockout and sample degradation and storage. However, we managed to set up three different library preparation methods for sequencing in Illumina. We also managed to decrease the hands on library preparation time from twelve to three hours, which allowed us to complete the outbreak investigation in just a few weeks. We also fine-tuned a simple bioinformatics workflow for the assembly of high-quality genomes in real-time. In order to allow other laboratories to learn from our experience, we released all of the library preparation and bioinformatics protocols publicly and distributed them to other laboratories of the South African Network for Genomics Surveillance (SANGS) consortium.
has issue date	2020-06-10(xsd:dateTime)
bibo:doi	10.1101/2020.06.10.144212
has license	biorxiv
sha1sum (hex)	f51c6dd9c64c64d413c5aacc8a85fe8b23d0adf6
schema:url	https://doi.org/10.1101/2020.06.10.144212
resource representing a document's title	Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic
schema:publication	bioRxiv
resource representing a document's body	covid:f51c6dd9c64c64d413c5aacc8a85fe8b23d0adf6#body_text
is schema:about of	named entity 'real-time' named entity 'SARS-CoV-2' named entity 'improve' named entity 'hospital' named entity 'encountered' named entity 'protocol' named entity 'Outbreak' named entity 'Investigation' named entity 'LABORATORIES' named entity 'WORLD' named entity 'GENOTYPING' named entity 'SET UP' named entity 'SIMPLE' named entity 'RELEASED' named entity 'NETWORK' named entity 'STARTED' named entity 'SOURCE' named entity 'PROVIDE' named entity 'GENOMES' named entity 'TO DECREASE' named entity 'ASSEMBLY' named entity 'PROTOCOLS' named entity 'DURBAN' named entity 'PATH' named entity 'FAST' named entity 'Phylogenetic analysis' named entity 'genomes' named entity 'genomes' named entity 'length' named entity 'outline' named entity 'South African' named entity 'outbreak investigation' named entity 'outbreak investigation' named entity 'case' named entity 'library' named entity 'path' named entity 'library' named entity 'genotype' named entity 'stockout' named entity 'South Africa' named entity 'genotyping' named entity 'stockout' named entity 'outbreak investigation' named entity 'genotype' named entity 'Illumina' named entity 'high-quality' named entity 'bioinformatics' named entity 'COVID-19 pandemic' named entity 'Durban' named entity 'genomes' named entity 'prospective study' named entity 'Genomics' named entity 'RNA extraction' named entity 'nosocomial' named entity 'probability' named entity 'Genomic sequencing' named entity 'Qubit' named entity 'genomes' named entity 'genome' named entity 'Illumina' named entity 'Durban' named entity 'outbreak investigation' named entity 'amplicon' named entity 'nasopharyngeal' named entity 'RNA' named entity 'Nanopore sequencing'

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