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

Detalhes bibliográficos
Autor(a) principal: Pillay, Sureshnee
Data de Publicação: 2020
Outros Autores: Giandhari, Jennifer, Tegally, Houriiyah, Wilkinson, Eduan, Chimukangara, Benjamin, Lessells, Richard, Moosa, Yunus, Mattison, Stacey, Gazy, Inbal, Fish, Maryam, Singh, Lavanya, Khanyile, Khulekani Sedwell, San, James Emmanuel, Fonseca, Vagner, Giovanetti, Marta, Alcantara, Luiz Carlos, Oliveira, Tulio de
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/43094
Resumo: KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa.
id CRUZ_71b07173e4dea42353518ace9e0a97f6
oai_identifier_str oai:www.arca.fiocruz.br:icict/43094
network_acronym_str CRUZ
network_name_str Repositório Institucional da FIOCRUZ (ARCA)
repository_id_str 2135
spelling Pillay, SureshneeGiandhari, JenniferTegally, HouriiyahWilkinson, EduanChimukangara, BenjaminLessells, RichardMoosa, YunusMattison, StaceyGazy, InbalFish, MaryamSingh, LavanyaKhanyile, Khulekani SedwellSan, James EmmanuelFonseca, VagnerGiovanetti, MartaAlcantara, Luiz CarlosOliveira, Tulio de2020-08-31T21:17:18Z2020-08-31T21:17:18Z2020PILLAY, Sureshnne; et al. Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic. Genes, v. 11, n. 949, p. 1-13, 2020.2073-4425https://www.arca.fiocruz.br/handle/icict/4309410.3390/genes11080949engMDPICOVID-19BioinformáticaSequenciamentoProtocolosIlluminaSARS-CoV-2SequencingIlluminaProtocolsCOVID-19BioinformaticsSARS-CoV-2Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemicinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleKwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa / Centre for AIDS Programme of Research in South Africa. Durban, South Africa / Department of Virology, National Health Laboratory Service, University of KwaZulu-Nata. Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa / Infectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal. Durban, Sputh Africa.Infectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal. Durban, Sputh Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa / Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratorio de Genetica Celular e Molecular. Belo Horizonte, MG, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil.KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa / Centre for AIDS Programme of Research in South Africa. Durban, South Africa / University of Washington. Department of Global Health. Seattle, WA, USA.The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (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. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/43094/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALVagnerFonseca_MartaGiovanettti_etal_IOC_2020.pdfVagnerFonseca_MartaGiovanettti_etal_IOC_2020.pdfapplication/pdf1766688https://www.arca.fiocruz.br/bitstream/icict/43094/2/VagnerFonseca_MartaGiovanettti_etal_IOC_2020.pdfdde3553d2bf3e572e912837fc5beecb2MD52TEXTVagnerFonseca_MartaGiovanettti_etal_IOC_2020.pdf.txtVagnerFonseca_MartaGiovanettti_etal_IOC_2020.pdf.txtExtracted texttext/plain59817https://www.arca.fiocruz.br/bitstream/icict/43094/3/VagnerFonseca_MartaGiovanettti_etal_IOC_2020.pdf.txt9a40f3cd045f4a4a57488faf810be2f2MD53icict/430942020-12-17 21:17:21.073oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352020-12-18T00:17:21Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.pt_BR.fl_str_mv Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
title Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
spellingShingle Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
Pillay, Sureshnee
COVID-19
Bioinformática
Sequenciamento
Protocolos
Illumina
SARS-CoV-2
Sequencing
Illumina
Protocols
COVID-19
Bioinformatics
SARS-CoV-2
title_short Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
title_full Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
title_fullStr Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
title_full_unstemmed Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
title_sort Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
author Pillay, Sureshnee
author_facet Pillay, Sureshnee
Giandhari, Jennifer
Tegally, Houriiyah
Wilkinson, Eduan
Chimukangara, Benjamin
Lessells, Richard
Moosa, Yunus
Mattison, Stacey
Gazy, Inbal
Fish, Maryam
Singh, Lavanya
Khanyile, Khulekani Sedwell
San, James Emmanuel
Fonseca, Vagner
Giovanetti, Marta
Alcantara, Luiz Carlos
Oliveira, Tulio de
author_role author
author2 Giandhari, Jennifer
Tegally, Houriiyah
Wilkinson, Eduan
Chimukangara, Benjamin
Lessells, Richard
Moosa, Yunus
Mattison, Stacey
Gazy, Inbal
Fish, Maryam
Singh, Lavanya
Khanyile, Khulekani Sedwell
San, James Emmanuel
Fonseca, Vagner
Giovanetti, Marta
Alcantara, Luiz Carlos
Oliveira, Tulio de
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Pillay, Sureshnee
Giandhari, Jennifer
Tegally, Houriiyah
Wilkinson, Eduan
Chimukangara, Benjamin
Lessells, Richard
Moosa, Yunus
Mattison, Stacey
Gazy, Inbal
Fish, Maryam
Singh, Lavanya
Khanyile, Khulekani Sedwell
San, James Emmanuel
Fonseca, Vagner
Giovanetti, Marta
Alcantara, Luiz Carlos
Oliveira, Tulio de
dc.subject.other.pt_BR.fl_str_mv COVID-19
Bioinformática
Sequenciamento
Protocolos
Illumina
SARS-CoV-2
topic COVID-19
Bioinformática
Sequenciamento
Protocolos
Illumina
SARS-CoV-2
Sequencing
Illumina
Protocols
COVID-19
Bioinformatics
SARS-CoV-2
dc.subject.en.pt_BR.fl_str_mv Sequencing
Illumina
Protocols
COVID-19
Bioinformatics
SARS-CoV-2
description KwaZulu-Natal Research Innovation and Sequencing Platform. School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal. Durban, South Africa.
publishDate 2020
dc.date.accessioned.fl_str_mv 2020-08-31T21:17:18Z
dc.date.available.fl_str_mv 2020-08-31T21:17:18Z
dc.date.issued.fl_str_mv 2020
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv PILLAY, Sureshnne; et al. Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic. Genes, v. 11, n. 949, p. 1-13, 2020.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/43094
dc.identifier.issn.pt_BR.fl_str_mv 2073-4425
dc.identifier.doi.none.fl_str_mv 10.3390/genes11080949
identifier_str_mv PILLAY, Sureshnne; et al. Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic. Genes, v. 11, n. 949, p. 1-13, 2020.
2073-4425
10.3390/genes11080949
url https://www.arca.fiocruz.br/handle/icict/43094
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/43094/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/43094/2/VagnerFonseca_MartaGiovanettti_etal_IOC_2020.pdf
https://www.arca.fiocruz.br/bitstream/icict/43094/3/VagnerFonseca_MartaGiovanettti_etal_IOC_2020.pdf.txt
bitstream.checksum.fl_str_mv 5a560609d32a3863062d77ff32785d58
dde3553d2bf3e572e912837fc5beecb2
9a40f3cd045f4a4a57488faf810be2f2
bitstream.checksumAlgorithm.fl_str_mv MD5
MD5
MD5
repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
_version_ 1813008968964898816

Registros relacionados