SARS-CoV-2 Genomics: Thailand Medical News Achieves Getting CRG To Standardize COVID-19 Data Analysis To Aid International Research Efforts
Source: SARS-CoV-2 Genomic Studies Mar 28, 2020 4 years, 7 months, 2 weeks, 3 days, 5 hours, 7 minutes ago
SARS-CoV-2 Genomic Studies: Thailand Medical News has managed to convinced more international genomic researchers to pay attention to the mutations and emerging strains of the SARS-CoV-2 coronavirus as in the past despite gene sequencing of strains that were detected in respective countries, many of these results were not properly compared and analyzed in detail to understand the evolutionary branches of the SARS-CoV-2 coronavirus and even the various differences of the clinical manifestations of these various emerging strains.
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There has been faked news and misinformation being disseminated by certain unqualified medical experts and even media that the SARS-CoV-2 coronavirus has not mutated and that there is only one strain, especially by the Washington Post
https://www.washingtonpost.com/health/the-coronavirus-isnt-mutating-quickly-suggesting-a-vaccine-would-offer-lasting-protection/2020/03/24/406522d6-6dfd-11ea-b148-e4ce3fbd85b5_story.html
Even when studies were already emerging that the virus was indeed mutating, and we at Thailand Medical News were calling for more attention to be paid to it to enhance drug, vaccine and diagnostic development, we were criticized by ignorant individuals.
https://www.thailandmedical.news/news/breaking-new-research-indicates-sars-cov-2-coronavirus-is-indeed-mutating-into-various-strains-that-have-specific-preference-of-attacking-human-host-
Most recently, health authorities in Iceland have reported that they have identified more than 40 different strains of the SAR-Cov-2 coronavirus.
https://nypost.com/2020/03/24/iceland-scientists-found-40-mutations-of-the-coronavirus-report-says/
https://www.msn.com/en-gb/news/coronavirus/scientists-in-iceland-claim-they-have-found-forty-mutations-of-the-coronavirus-and-admit-seven-cases-can-be-traced-back-to-a-football-match-in-england/ar-BB11DpwG?li=BBoPRmx
Genomic and virology researchers from the Centre for Genomic Regulation (CRG) have decided to heed our call and have launched a new database to advance the international research efforts studying COVID-19.
The publicly-available, free-to-use resource can be used by researchers from around the world to study how different variations of the virus grow, mutate and make proteins. (https://biocorecrg.github.io/covid/) (
k">covid.crg.eu)
Dr Eva Novoa, a researcher at the CRG in Barcelona said , "Scientists are working round the clock to understand SARS-CoV-2, the virus causing COVID-19, so that we can find its weak spots and beat it. A huge amount of scientific data is being published around the world."
Dr Novua however warned, "However, some of the technologies we use to study SARS-CoV-2, such as nanopore RNA sequencing, are so new that the results of one paper aren't comparable to another due to the patchwork of different standards and methodologies used. We are taking all this data and analyzing it so that it meets a more universally comparable standard. This will help researchers more quickly and accurately spot the strengths and weaknesses of the coronavirus."
The researchers at CRG commented, “It is interesting that a small entity such as Thailand Medical News, with just a couple of medically trained personnel have been analyzing the situation in detail and doing their own meta-analysis of existing research data and making interesting hypothetical conclusions that can contribute to researchers to focus into the right directions.”
In order to understand how the coronavirus grows, mutates and replicates, scientists have to sequence the RNA of COVID-19. The RNA sequence reveals crucial information about the proteins the virus makes to invade human cells and replicate, which in turn informs governments on the infectiousness and severity of the pandemic.
It must be noted that traditional sequencing tools can take a long time to provide results. In recent years, sequencing data in real time has become a reality thanks to the use of nanopore sequencing technologies, revolutionizing genomics research and disease outbreak monitoring. Nanopore sequencing provides scientists and clinicians with immediate access to the DNA and RNA sequence information of any living cell in real-time, enabling a rapid response against the threat of a pandemic.
Also, the raw data produced by nanopore sequencing is highly complex. Scientists and clinicians currently lack systematic guidelines for the reproducible analysis of the data, limiting the vast potential of the nascent technology.
In order to standardize the analysis of publicly available SARS-CoV-2 nanopore sequencing data, researchers at the Centre for Genomic Regulation (CRG) in Barcelona are using MasterOfPores, a computer program developed by the group of Eva Novoa and CRG Bioinformatics Unit. The software was first described last week in
Frontiers in Genetics.
Dr Julia Ponomarenko, Head of the Bioinformatics Unit at the CRG added, "The internet and an increasing culture of open science, data sharing and preprints have transformed the research landscape. Infrastructure that would take months to set up to research an emerging virus can now be done in just a few days owing to novel scientific computing approaches."
The MasterOfPores programme can be executed on any Unix-compatible OS on a computer, cluster or cloud without the need of installing any additional software or dependencies, and is freely available in Github. The publicly-available, free-to-use resource has currently analysed 3TB of SARS-CoV-2 nanopore RNA sequencing data. The CRG researchers will continue to update the resource with new data as soon as it becomes available.
CRG and also four other genomic and research labs located in the US, Taiwan, Australia and UK will also be working with Thailand Medical News on another project to tests the efficacy of various TCM formulations and natural herbs to stop viral replication, on the various emerging strains of the SARS-CoV-2 coronavirus from both a genomic aspect and also via in vitro studies.
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