Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
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 b...
| Main Authors: | , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-08-01
|
| Series: | Genes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4425/11/8/949 |
| _version_ | 1797557549217611776 |
|---|---|
| author | Sureshnee Pillay Jennifer Giandhari Houriiyah Tegally Eduan Wilkinson Benjamin Chimukangara Richard Lessells Yunus Moosa Stacey Mattison Inbal Gazy Maryam Fish Lavanya Singh Khulekani Sedwell Khanyile James Emmanuel San Vagner Fonseca Marta Giovanetti Luiz Carlos Alcantara Tulio de Oliveira |
| author_facet | Sureshnee Pillay Jennifer Giandhari Houriiyah Tegally Eduan Wilkinson Benjamin Chimukangara Richard Lessells Yunus Moosa Stacey Mattison Inbal Gazy Maryam Fish Lavanya Singh Khulekani Sedwell Khanyile James Emmanuel San Vagner Fonseca Marta Giovanetti Luiz Carlos Alcantara Tulio de Oliveira |
| author_sort | Sureshnee Pillay |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T17:18:32Z |
| format | Article |
| id | doaj.art-b6bf0bd69412487e9fcd4fb63e5f9947 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T17:18:32Z |
| publishDate | 2020-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-b6bf0bd69412487e9fcd4fb63e5f99472023-11-20T10:25:57ZengMDPI AGGenes2073-44252020-08-0111894910.3390/genes11080949Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a PandemicSureshnee Pillay0Jennifer Giandhari1Houriiyah Tegally2Eduan Wilkinson3Benjamin Chimukangara4Richard Lessells5Yunus Moosa6Stacey Mattison7Inbal Gazy8Maryam Fish9Lavanya Singh10Khulekani Sedwell Khanyile11James Emmanuel San12Vagner Fonseca13Marta Giovanetti14Luiz Carlos Alcantara15Tulio de Oliveira16KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaInfectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaLaboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro 21045-900, BrazilLaboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, BrazilKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South AfricaThe 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.https://www.mdpi.com/2073-4425/11/8/949sequencingSARS-CoV2IlluminaprotocolsCOVID-19bioinformatics |
| spellingShingle | Sureshnee Pillay Jennifer Giandhari Houriiyah Tegally Eduan Wilkinson Benjamin Chimukangara Richard Lessells Yunus Moosa Stacey Mattison Inbal Gazy Maryam Fish Lavanya Singh Khulekani Sedwell Khanyile James Emmanuel San Vagner Fonseca Marta Giovanetti Luiz Carlos Alcantara Tulio de Oliveira Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic Genes sequencing SARS-CoV2 Illumina protocols COVID-19 bioinformatics |
| title | 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_short | 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 |
| topic | sequencing SARS-CoV2 Illumina protocols COVID-19 bioinformatics |
| url | https://www.mdpi.com/2073-4425/11/8/949 |
| work_keys_str_mv | AT sureshneepillay wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT jennifergiandhari wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT houriiyahtegally wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT eduanwilkinson wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT benjaminchimukangara wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT richardlessells wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT yunusmoosa wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT staceymattison wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT inbalgazy wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT maryamfish wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT lavanyasingh wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT khulekanisedwellkhanyile wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT jamesemmanuelsan wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT vagnerfonseca wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT martagiovanetti wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT luizcarlosalcantara wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic AT tuliodeoliveira wholegenomesequencingofsarscov2adaptingilluminaprotocolsforquickandaccurateoutbreakinvestigationduringapandemic |