Sequencing the COVID-19 virus genome
“If you know the enemy and know yourself, you need not fear the result of a hundred battles.” ― Sun Tzu, ‘The Art of War’
By comparing the genetic data (or genomes) of COVID-19 samples that emerge in different parts of the world, scientists can determine the relationships between different strains of the virus and track the spread of disease outbreaks. Genome sequences can also be used to develop diagnostic tests and identify stable regions for vaccine design.
The team in the UCD Conway Institute Genomics Core recently worked in collaboration with the UCD National Virus Reference Laboratory (NVRL) to obtain the genomes of the SARS-CoV-2 virus from the first COVID-19 patient samples in Ireland.
Professor Brendan Loftus, Director of the facility, Fellow in UCD Conway Institute and Professor of Comparative Genomics in UCD School of Medicine said, “We were very fortunate to be able to assist the NVRL in obtaining viral sequences from some of the initial COVID-19 patient samples in Ireland, which was a real team effort.
To do this, we used a portable MinION - not to be confused with the little yellow guys from Universal Studios! - real-time DNA sequencing device. This portable device from Oxford Nanopore Technologies is about the same size as an iPhone. It has been used in previous global virus outbreak studies such as Ebola and Zika.”
By comparing the genetic data (or genomes) of COVID-19 samples that emerge in different parts of the world, scientists can determine the relationships between different strains of the virus and track the spread of disease outbreaks. Genome sequences can also be used to develop diagnostic tests and identify stable regions for vaccine design.
The team in the UCD Conway Institute Genomics Core recently worked in collaboration with the UCD National Virus Reference Laboratory (NVRL) to obtain the genomes of the SARS-CoV-2 virus from the first COVID-19 patient samples in Ireland.
Professor Brendan Loftus, Director of the facility, Fellow in UCD Conway Institute and Professor of Comparative Genomics in UCD School of Medicine said, “We were very fortunate to be able to assist the NVRL in obtaining viral sequences from some of the initial COVID-19 patient samples in Ireland, which was a real team effort.
To do this, we used a portable MinION - not to be confused with the little yellow guys from Universal Studios! - real-time DNA sequencing device. This portable device from Oxford Nanopore Technologies is about the same size as an iPhone. It has been used in previous global virus outbreak studies such as Ebola and Zika.”
Alison Murphy and Catherine Moss, Senior Technical Officers in the Genomics Core carried out the technical aspects of the sequencing protocol. Commenting on the process, Alison Murphy said, “We have been offering Nanopore sequencing on our MinION device since 2016. After initial support from Catherine in the planning stages of the process, I then worked with Dr Michael Carr, NVRL on the steps from library preparation through to sequencing on the MinION device.
Michael and I used a PCR tiling approach based on the ARTIC Network protocol to generate sequencing libraries, which takes a significant amount of time. This approach has been proven to have high sensitivity and works directly from clinical samples. It has been adopted by multiple research centres worldwide during this pandemic.
After library construction, it is a relatively rapid process - about six hours - to get the viral sequence data. The MinION device was connected to a dedicated computer in the laboratory of Professor Ken Wolfe to do this.
The resulting viral sequences have been used to inform surveillance and epidemiology through GISAID, a global initiative on sharing all influenza data.”
Ken Wolfe, Professor of Genomic Evolution in UCD School of Medicine and Fellow in UCD Conway Institute has recently been using MinION to sequence genomes of some yeast species for research being carried out both in his laboratory and in that of Professor Geraldine Butler.
Michael and I used a PCR tiling approach based on the ARTIC Network protocol to generate sequencing libraries, which takes a significant amount of time. This approach has been proven to have high sensitivity and works directly from clinical samples. It has been adopted by multiple research centres worldwide during this pandemic.
After library construction, it is a relatively rapid process - about six hours - to get the viral sequence data. The MinION device was connected to a dedicated computer in the laboratory of Professor Ken Wolfe to do this.
The resulting viral sequences have been used to inform surveillance and epidemiology through GISAID, a global initiative on sharing all influenza data.”
Ken Wolfe, Professor of Genomic Evolution in UCD School of Medicine and Fellow in UCD Conway Institute has recently been using MinION to sequence genomes of some yeast species for research being carried out both in his laboratory and in that of Professor Geraldine Butler.
“We have a dedicated computer with the necessary software for MinION sequencing already set up. We were delighted to be able to offer some assistance to our colleagues here in the Institute and in the NVRL.”
Dr Kevin Byrne and PhD student, Eoin O Cinnéide helped with the sequencing itself. Kevin and Dr Gabriel Gonzalez, NVRL clinical bioinformatician installed an additional software module from ARTIC Network called Rampart to enable monitoring the quality of the sequencing results in real time as the data was coming in from the MinION instrument.
Commenting on the results, Dr Michael Carr said, “The first Irish SARS-CoV-2 genomes revealed that one was 100% identical to the original genome from Wuhan city, which surprised me as RNA viruses are notoriously variable. Others were related to a European clade from individuals with travel history to northern Italy. The genetic stability gives hope for therapeutic and prophylactic options."
Dr Gabriel Gonzalez added, “Overall, the virus is remarkably conserved from our data and that from other laboratories with only 7 or 8 branches in the tree of all known sequences. This speaks to a recent spillover from an animal that, based on available genetic data, is likely a horseshoe bat betacoronavirus.”
Professor Brendan Loftus believes, “This is a great example of the scientific community, in diagnostic and academic settings, coming together and making strides in scientific research at a time of global need. It highlights the significant potential for collaboration that perhaps can be tapped into when this crisis passes.”
About GISAID - Global Initiative on Sharing All Influenza Data (https://www.gisaid.org/)
GISAID promotes the international sharing of all influenza virus data to enable seasonal and pandemic preparedness. Genomic data can inform the incidence, distribution, and possible control of diseases and other factors relating to health. The map of 2499 genomes of novel coronavirus sampled between Dec 2019 and Mar 2020 are available from GISAID data online - https://nextstrain.org/ncov
About Artic Network (https://artic.network/)
This project is developing an end-to-end system for processing samples from viral outbreaks to generate real-time epidemiological information that is interpretable and actionable by public health bodies. The ARTIC network is making available a set of materials to assist groups in sequencing viruses including a set of primers, laboratory protocols, bioinformatics tutorials and datasets.
This project is developing an end-to-end system for processing samples from viral outbreaks to generate real-time epidemiological information that is interpretable and actionable by public health bodies. The ARTIC network is making available a set of materials to assist groups in sequencing viruses including a set of primers, laboratory protocols, bioinformatics tutorials and datasets.
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