GISAID comments on the speculations surrounding data availability

Recent discussions surrounding early hCoV-19 sequence data associated with a manuscript submitted by the researchers at the China CDC have been clouded by speculation regarding the status of the data. Here we clarify the current status of that data, and take this opportunity to reiterate the general data sharing policies at GISAID.

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. 

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.

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).  

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:

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. 

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

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)

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.

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.