Updates of GISAID data, 23 December 2021

Routine updates to improve data in GISAID

GISAID is committed to near-instant processing and release of genome and metadata to ensure its platform continues to make emerging outbreak information accessible at unprecedented speeds and scale. From time to time, laboratories will increase the speed with which they generate data and submit to GISAID, for instance when new Variants of Interest or Variants of Concern are designated by the WHO. With this increased speed, the need to check for errors in genomic sequence data or metadata also increases. 

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Data quality control procedures, 15 August 2021

GISAID EpiCoV™ data quality control procedures and B.1.621 (Mu) monitoring

In late July 2021, GISAID confirmed with public health authorities its procedures for the quality control of gaps in genomic sequences that cause frameshifts and other genomic changes. Social media discussions mistakenly suggested B.1.621 (Mu) genome sequences could have been kept from release due to a 4nt deletion in ORF3A that results in a premature stop codon.

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Clade and lineage nomenclature, 2 March 2021

Clade and lineage nomenclature aids in genomic epidemiology of active hCoV-19 viruses

Due to the naturally expanding phylogenetic diversity of hCoV-19 viruses in late February 2020, GISAID named for consistent reporting larger clades, based on marker mutations within 6 high-level phylogenetic groupings from the early split of S and L, to the further evolution of L into V and G and later of G into GH, GRY (Alpha) and GK (Delta).  

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New swine flu enters the watchlist, 7 July 2020

New swine flu enters the watchlist

Virus surveillance in animals is an important aspect of pandemic preparedness to know what is out there and could cause zoonotic infections (jumps from animals to humans) or even represent pandemic threats. Colleagues have concluded a surveillance study in pigs and identified a new reassortant H1N1 swine flu that shows the minimal characteristics for a virus with pandemic potential.

Here are some important facts to consider:

Clades of hCoV-19, 13 April 2020

Discussion on different types or clades of the hCoV-19 virus and their origin

As the outbreak evolves over time and more data becomes available, several colleagues have analyzed and proposed different "types" of the virus and their origin. Depending on choice of definitions one can classify the circulating virus strains into a different number of clades based on genetic variants. These are part of the natural evolution of the virus currently not known to be associated with any differences in virulence. 

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U.S. Department of State request for comments - No. 10789, 20 September 2019

GISAID Comments on the Implications of Access and Benefit- Sharing (ABS) Regimes on Global Health and Biomedical Research

The Global Initiative on Sharing All Influenza Data responds to the invitation by the U.S. Department of State (DOS) and comments on the effects of the Nagoya Protocol and other ABS implementation on public health systems, and emphasizes the collective global benefit of robust influenza virus surveillance which is achieved in part through the sharing of all influenza GSD in a timely manner.  read more

WHO Report on the Public Health Implications of Nagoya Protocol, 13 May 2019

GISAID's Comments on the WHO Report on the Public Health Implications of Implementation of the Nagoya Protocol

The Report on the "public health implications of implementation of the Nagoya Protocol" raises a number of major concerns. While the Report speaks about ‘principles of global public health’ enshrined in the Constitution of the World Health Organization (WHO) it does not state one of its key objectives that is '… to eradicate epidemic, endemic and other diseases;'. (see No.8)  read more

GISAID’s Submission to CBD Notification 2017-037

GISAID's Position Paper on Digital Sequence Information on Genetic Resources 

GISAID responds to an invitation by the CBD Secretariat to comment on any potential implications of the use of digital sequence information on genetic resources for the three objectives of the Convention and the Nagoya Protocol, as communicated in notification 2017-37 Ref.:SCBD/SPS/DC/VN/KG/jh/86500 of 25 April 2017. read more

re3data.org and DataCite affirm open access designation, 4. September 2017

Editorial Board affirms Open Access designation of GISAID

re3data.org and DataCite, the world’s leading provider of digital object identifiers (DOI) for research data, affirmed the designation of access to GISAID's database and data as Open Access. A persistent link for this designation has been assigned to GISAID for citation purposes.  read more

GloPID-R Principles for Data Sharing in Public Health Emergencies, 2. May 2017

GISAID's Comments on GloPID-R Principles for Data Sharing in Public Health Emergencies

GISAID responded to an invitation posted on the homepage of the Global Research Collaboration for Infectious Disease Preparedness (GloPID-R) to comment on a document entitled ‘Data Sharing Principles’ indicating its gratification that the seven key principles of GloPID-R are nearly identical with the principles underlying the sharing mechanism of the GISAID Initiative, introduced in 2008, and being indispensable the influenza community since. read more

Session of the 140th WHO Executive Board, 27. January 2017

Germany’s Statement on the Review of the Pandemic Influenza Preparedness Framework

We welcome the recommendation to further align capacity building activities under the PIP Framework to IHR implementation activities. Germany will maintain its commitment to global influenza preparedness and to the PIP Framework. One important pillar of this commitment is our partnership with GISAID. We will continue to host the database EpiFlu™ as an important tool for sharing of genetic sequences data in the spirit of the PIP Framework, ensuring fair, timely and transparent access to GSD in a sustainable way.  read more

WHO PIP Framework Review Group 2016, 25. September 2016

GISAID's Comments on the Preliminary Findings of the PIP Framework Review

Difficulties which the GISAID Initiative has experienced in developing dialogue with the PIP Secretariat (and the Advisory Group) exemplify a lack of transparency and openness with some key stakeholders, engendering a lack of trust in contrast to that enjoyed by GISAID with GISRS and the GIP. While raised on numerous occasions, this problem has never been responded to in a satisfactory manner that would indicate the concerns raised are actually addressed. read more

WHO Special Session of the PIP Advisory Group, 13. October 2015

Germany’s Statement on Substantive Issues and Concerns Regarding the PIP Framework and its Implementation 

The Federal Republic of Germany entered, in 2010, into a public-private partnership with the GISAID Initiative and has since hosted the publicly-accessible EpiFlu™ database, employing a unique sharing mechanism which ensures that inherent rights (e.g. IPR) of contributors of GSD are not forfeit. Access to EpiFlu™ is free and open to anyone who positively identifies himself or herself and agrees to respect the rights of contributors. This ensures fair and transparent sharing of GSD, making certain that all users mutually respect the rights of contributors and other users. Importantly, this mechanism provides contributors with the necessary incentive to rapidly share GSD, in the interests of Global Public Health.  read more

Steven Salzberg Blog, 2. October 2011

Clarifying Misconceptions Regarding Influenza Research, GISAID, and the Role of the US Centers for Disease Control and Prevention

We read with interest the October 2, 2011 opinion piece by Steven Salzberg titled, Is The Government Hiding Something About Swine Flu?, which was published on various internet blogs by Dr. Salzberg.  We fully support his right to express his opinions, and applaud his efforts to raise public awareness concerning influenza research and prevention.  Unfortunately, however, Dr. Salzberg’s  opinion piece contains certain fundamental misstatements and omissions that make his article dangerously misleading.  read more