Sharing of pathogen genomic data
27 April 2022
In the past 20 years sequencing technologies progressively became a fundamental tool for scientific research, especially in the biomedical field. The recent development of high throughput sequencing methods (NGS), represented a major breakthrough in this respect. Indeed, apart from a sensible reduction in sequencing costs and a massive increase in the throughput of sequencing, these technologies also provided the foundations for the development of novel analytical methods and approaches and a more “quantitative” and data driven study of biological phenomena.
The interpretation of sequencing data depends mainly on the comparison with pre-existing sequences databases or on the application of analysis/bioinformatics methods which apply interpretative models based on “reference” sequences.
Data sharing is a key aspect of scientific research and in light of the considerations highlighted above, sharing of sequencing data is fundamental to favor a correct and unbiased interpretation.
The last two years of COVID-19 pandemic have highlighted how pathogen genome sequencing represents one of the first lines of defense to monitor the evolution of pathogens and limit the spread of more dangerous variants, demonstrating once more how data sharing is essential for both research and public health communities. This notwithstanding we still experience several issues and limitations in the sharing of SARS-CoV-2 genome sequence data.
For a more comprehensive overview of the importance of data sharing in pathogen genomic surveillance we invite our readers to refer to a recently published white paper by Cochrane et al that provides a comprehensive overview of the most important challenges and issues for the effective sharing of pathogen genome sequencing data. The paper is available at the following link.
Read more The interpretation of sequencing data depends mainly on the comparison with pre-existing sequences databases or on the application of analysis/bioinformatics methods which apply interpretative models based on “reference” sequences.
Data sharing is a key aspect of scientific research and in light of the considerations highlighted above, sharing of sequencing data is fundamental to favor a correct and unbiased interpretation.
The last two years of COVID-19 pandemic have highlighted how pathogen genome sequencing represents one of the first lines of defense to monitor the evolution of pathogens and limit the spread of more dangerous variants, demonstrating once more how data sharing is essential for both research and public health communities. This notwithstanding we still experience several issues and limitations in the sharing of SARS-CoV-2 genome sequence data.
For a more comprehensive overview of the importance of data sharing in pathogen genomic surveillance we invite our readers to refer to a recently published white paper by Cochrane et al that provides a comprehensive overview of the most important challenges and issues for the effective sharing of pathogen genome sequencing data. The paper is available at the following link.
Prevalence of SARS-CoV-2 variants in Italy (ISS report n. 18 and March 7th 2022 ISS Flash Survey)
08 April 2022
The I-Co-Gen platform by the Italian National Institute of Health (ISS) is the most up to date and reliable system for the collection and analysis of SARS-CoV-2 genome sequencing data in Italy. Based on the data processed through I-Co-Gen, the Italian National Institute of Health (ISS), supported by the Bruno Kessler Foundation and in collaboration with the Italian Ministry of Health, the Regional administrations and the Autonomous Provinces (PPAA), have launched a coordinated effort to monitor the spread of SARS-CoV-2 variants in Italy. Results are released periodically in the form of brief reports (further details here, Italian only).
This highlight provides a brief overview of the main results from the most recent report (data from March 7th 2022). Data from the previous report (data from January 31st 2022) are also included for the sake of comparison.
Read more This highlight provides a brief overview of the main results from the most recent report (data from March 7th 2022). Data from the previous report (data from January 31st 2022) are also included for the sake of comparison.
ELIXIR-CONVERGE WP9 Webinar
15 March 2022
March 30th 2022 - h. 10:00 AM-12:00 PM (CEST) - Online, Registration required
The main goal of this webinar is to address the legal aspects involved in the mobilization of SARS-CoV-2 genomic data in Europe. The seminar is specifically designed for organizations and people responsible for data brokering across healthcare systems, research infrastructures and publicly accessible data sharing platforms.
The primary focus of the seminar is to illustrate a collection of examples that highlight how legal aspects come into play when genetic, personal and phenotypic data are processed and shared in different Countries.
More information about the event outline and the registration form is available at the following link.
Read more The main goal of this webinar is to address the legal aspects involved in the mobilization of SARS-CoV-2 genomic data in Europe. The seminar is specifically designed for organizations and people responsible for data brokering across healthcare systems, research infrastructures and publicly accessible data sharing platforms.
The primary focus of the seminar is to illustrate a collection of examples that highlight how legal aspects come into play when genetic, personal and phenotypic data are processed and shared in different Countries.
More information about the event outline and the registration form is available at the following link.
Prevalence of SARS-CoV-2 variants in Italy (January 17th and January 31st 2022 ISS Flash Surveys)
18 February 2022
The I-Co-Gen platform developed by the Italian National Institute of Health (ISS), and released in April 2021, is currently the most up to date and reliable system for the collection and analysis of SARS-CoV-2 genome sequencing data in Italy. Based on the data processed through I-Co-Gen, the Italian National Institute of Health (ISS), supported by the Bruno Kessler Foundation and in collaboration with the Italian Ministry of Health, the Regional administrations and the Autonomous Provinces (PPAA), have launched an ongoing and coordinated effort to monitor the spread of SARS-CoV-2 variants in Italy. Results are released periodically in the form of brief reports (further details here, Italian only).
This highlight provides a brief overview of the main results from the most recent reports (data from January 17th and January 31st 2022). Data from the previous report (data from January 3rd 2022) are also included for the sake of the comparison.
Read more This highlight provides a brief overview of the main results from the most recent reports (data from January 17th and January 31st 2022). Data from the previous report (data from January 3rd 2022) are also included for the sake of the comparison.
The I-Co-Gen platform developed by the Italian National Institute of Health (ISS), and released in April 2021, is currently the most up to date and reliable system for the collection and analysis of SARS-CoV-2 genome sequencing data in Italy. Based on the data processed through I-Co-Gen, the Italian National Institute of Health (ISS), supported by the Bruno Kessler Foundation and in collaboration with the Italian Ministry of Health, the Regional administrations and the Autonomous Provinces (PPAA), have launched an ongoing and coordinated effort to monitor the spread of SARS-CoV-2 variants in Italy. Results are released periodically in the form of brief reports (further details here, Italian only).
This highlight provides a brief overview of the main results presented in the most recent report (data from January 3rd 2022). Data from the previous reports (data from December 6th and December 20th 2021) are also included to facilitate the comparison.
Read more This highlight provides a brief overview of the main results presented in the most recent report (data from January 3rd 2022). Data from the previous reports (data from December 6th and December 20th 2021) are also included to facilitate the comparison.
Prevalence of SARS-CoV-2 variants in Italy (ISS report n. 15 and December 20th 2021 ISS Flash Survey)
14 January 2022
The I-Co-Gen platform developed by the Italian National Institute of Health (ISS), and released in April 2021, is currently the most up to date and reliable system for the collection and analysis of SARS-CoV-2 genome sequencing data in Italy. Based on the data incorporated in I-Co-Gen, the Italian National Institute of Health (ISS), supported by the Bruno Kessler Foundation and in collaboration with the Italian Ministry of Health, the Regional administrations and the Autonomous Provinces (PPAA), have started an ongoing and coordinated effort for the accurate mapping of the spread of SARS-CoV-2 variants in Italy. Results are released periodically in the form of brief reports (further details here).
This highlight provides a brief overview of the main results presented in the most recent reports (data from December 6th and December 20th 2021). Data from the previous report (September 28th 2021) are also included to facilitate the comparison.
ISS decided to perform two different Flash Surveys in December, to monitor more carefully the spread of the Omicron variant in Italy. This highlight includes both.
Read more This highlight provides a brief overview of the main results presented in the most recent reports (data from December 6th and December 20th 2021). Data from the previous report (September 28th 2021) are also included to facilitate the comparison.
ISS decided to perform two different Flash Surveys in December, to monitor more carefully the spread of the Omicron variant in Italy. This highlight includes both.