One year since first genomes of SARS-CoV-2 released to the world 10 January 2020 00:41UTC

One year ago, critical public health responses around the globe were kicked off, when China CDC shared via GISAID the first SARS-CoV-2 whole-genomes and associated data. 

This curated, high-quality data made available through GISAID permitted the initiation of the development of the first vaccines, diagnostic tests, and other responses at unprecedented speed, including the first vaccines to be approved and made available (Polack et al N Engl J Med 2020), and development of the first NAAT and RT-PCR-based molecular tests to detect the pandemic coronavirus (Bohn et al Clin Chem Lab Med 2020). 

Comment on recent variants and spike protein changes

As seen on many occasions before, mutations are naturally expected for viruses and are most often simply neutral regional markers useful for contact tracing. The changes seen have rarely affected viral fitness and almost never affected clinical outcome but the detailed effects of these mutations remain to be determined fully. Changes in the spike protein have relevance for potential effects on both host receptor as well as antibody binding with possible consequences for infectivity, transmission potential and antibody and vaccine escape. Actual effects need to be measured and verified experimentally.

As has become evident, these few S gene mutations and some deletions are found in multiple genomic contexts (different clades in different countries) that may be an early indication for some potential advantage for these viruses but needs to be verified and does not necessarily mean change in clinical severity or transmission efficiency.  > read more    

UK reports new variant, termed VUI 202012/01

The United Kingdom reported a new variant, termed VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01). It was defined by multiple spike protein changes (deletion 69-70, deletion 145, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H). An increasing fraction in Southern England (all from clade GR) share several of these changes and a handful have been seen through imports in other countries. 

As seen on many occasions before, changes are naturally expected for viruses and are most often simply neutral regional markers useful for contact tracing. The changes seen have rarely been affecting viral fitness and almost never affect clinical outcome but the detailed effects of these changes remain to be determined fully.

> read more    

New hCoV-19 variant in Europe, part of natural evolution

The newest variant of the coronavirus responsible for COVID-19 circulating in Europe features an A222V change in the spike glycoprotein and is designated as clade GV, part of the clade G. The change is not at the receptor binding site but pointing away from it and may, if anything, affect stability of the protein complex with a less pronounced effect than D614G based on its structural position and also not expected to change antibody binding much, depending on the site where the antibody binds.

It's current strong rise within Europe and the age group bias towards young adults could simply point to a founder effect. A222V occurred about 11k times in GISAID submitted genomes (out of 167k) and apart from a handful of exceptions from travel imports, had been restricted to Europe so far.

Low human health risk of hCoV-19 mutants from mink farms

Mink and other mustelids such as ferrets can be infected relatively easily with hCoV-19. It is not clear why the virus is so contagious in these animals. What is clear is that when viruses infect farmed mink - housed at high densities and in large numbers - this may result in massive virus amplification, posing a high infection risk to humans and animals alike.

During virus amplification in mink, natural selection (“adaptation”) may occur which can be observed by the emergence of mutations that are not seen in human viruses. These mutations are selected because they apparently provide a benefit to the virus in mink. It is important to note that if these mutations would also provide a benefit in humans (resulting in enhanced virulence or transmission) they would have already been naturally selected during infection of (millions of) infected humans hosts. The fact that mink virus variants have not been seen in humans through chains of transmission provides convincing scientific evidence that mutant viruses from mink provide little to none additional health risk to humans.

> read more    

First new arrivals of highly pathogenic avian influenza H5 in the 2020-2021 winter in Europe

Highly pathogenic avian influenza viruses of the H5N8 and H5N1 subtypes were detected in the Netherlands in October 2020. The HA genes of the two viruses are closely related, but the other genes of the H5N1 viruses appear to originate from other virus lineages circulating in Eurasia. The earliest virus detections were on 16 October in Eurasian wigeons, a long-distance migrant, and four full virus genomes were uploaded to GISAID by late October.

The virus genome sequences are suggestive for new virus introductions into the EU, different from the outbreaks of last winter. Previously, scientists from the Global Consortium for H5N8 and Related Influenza Viruses used GISAID data to investigate the role of migratory wild birds.

> read more    

Recommended composition of influenza virus vaccines for use in the 2021 Southern Hemisphere influenza season announced

Experts taking part in the WHO vaccine composition and information meeting (VCM) between 16-24 September 2020, organized by the WHO Global Influenza Programme, announced on 25. September the recommended components for vaccines for the 2021 Southern Hemisphere influenza season.

These recommendations are used by the national vaccine regulatory agencies and the pharmaceutical companies to develop, produce and license influenza vaccines.

read more:

GISAID wishes Naomi Komadina a Happy 70th Birthday

The Global Initiative congratulates Naomi Komadina, Head of Bioinformatics at WHO Collaborating Centre for Reference and Research on Influenza at the Victorian Infectious Diseases Reference Laboratory (VIDRL) in Melbourne and thanks her for her substantial contributions to GISAID from the start of its incredible journey.

Naomi’s steadfast commitment to responsible data sharing and her technical knowledge passed on to countless participants in GISAID educational workshops around the world, contributed to the global collaboration that enabled GISAID to perform its essential role during outbreaks, such as the new H1N1 influenza virus in 2009 and the emerging coronavirus responsible for the current COVID-19 pandemic.

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 present pandemic threats. Researchers 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.

Reassortment of viruses at the animal-human interface continues to be a serious problem. The G4 virus is one of several swine viruses with zoonotic potential in the world that should be watched closely.

Here are some important facts to consider: 

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

Due to the naturally expanding genetic diversity of hCoV-19 viruses, GISAID introduced a nomenclature system for major clades, developed by Sebastian Maurer-Stroh et al, based on marker mutations within 8 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, GR and GV, and more recently GR into GRY.

GISAID clades are augmented with more detailed lineages assigned by the Phylogenetic Assignment of Named Global Outbreak LINeages (Pango lineages) tool, aiding in the understanding of patterns and determinants of the global spread of the pandemic strain causing COVID-19. A third effort uses a Year-Letter nomenclature to facilitate discussion of large-scale diversity patterns of hCoV-19 and label clades that persist for at least several months and have significant geographic spread.  > read more

GISAID Comments on the Discussion of 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.

It is important to note that there is currently not enough data from the early outbreak period to interpret the early history of global transmissions from few genomes in detail. Links that seem directly connected now are likely to be connected via other cases also from other countries not sampled and sometimes can be connected differently later with more data.                              

> read GISAID's Comments

Recommended composition of influenza virus vaccines for use in the 2020-2021 Northern Hemisphere Influenza Season announced

(Geneva, Switzerland) An advisory group of experts taking part in a meeting organized by the WHO Global Influenza Programme between 24-27 February 2020 analyzed influenza virus surveillance data generated by the WHO Global Influenza Surveillance and Response System (GISRS), and issued on 28 February 2020, recommendations on the composition of the influenza vaccines for the following influenza season.

These recommendations are used by the national vaccine regulatory agencies and the pharmaceutical companies to develop, produce and license influenza vaccines.

read more:

China shares first genome sequences of the newly emerging coronavirus

Laboratories around the world are generating in an unprecedented manner, more and more genome sequences and related clinical and epidemiological data associated with the newly emerging coronavirus (hCoV-19) rapidly made available via GISAID. The pandemic virus was first identified in late December 2019 in Hubei Province, where patients were suffering from respiratory illnesses such as pneumonia. Since then, hCoV-19 is detected across the globe.

The genome sequences of hCoV-19 are crucial to design and evaluate diagnostic tests, to track and trace the ongoing outbreak and to identify potential intervention options.

Indonesia hosts GISAID Bioinformatics Training Workshop at NIHRD

(Jakarta) Indonesia's National Institute of Health Research and Development (NIHRD) and GISAID held a influenza bioinformatics training workshop from 4-8 November. Hands-on training was provided by GISAID DTG members from the WHO Collaborating Centre for Reference and Research on Influenza, Melbourne and the Bioinformatics Institute (BII), Singapore.

Participants from across Indonesia were trained on a new computational pipeline introduced by BII to generate consensus sequences from next generation sequencing data, and on the GISAID platform to monitor complex epidemiological relationships among circulating animal and human influenza viruses and the detection and interpretation of evolutionary changes. see the Report

World Flu Day 2019:  China’s Campaign for Flu Awareness and Academic Conference

The Chinese Center for Disease Control and Prevention hosted in Beijing the launch of the Popular Science Promotion Campaign for Flu Awareness & Academic Conference in Celebration of the 2nd World Flu Day on 1. November 2019. 

Under the motto 'Know Flu, Prevent Flu, Beat Flu' researchers agreed to unite in a push for stronger political will across the globe, calling for the continuing support of influenza prevention and control. The event welcomed 800 participants who reflected on the progress made since the 2009 H1N1 Pandemic.

> see Xinhua News (2019) and The Lancet (2018) 

Vicki Gregory
1968-2019

With deep sadness we announce the loss of Vicki Gregory, a member of our scientific family and dear friend. Vicki was a founding member of GISAID’s Database Technical Group playing a key role in providing scientific guidance for the development of GISAID’s EpiFlu database.

Vicki was held in high regard by colleagues around the world for her contribution to influenza surveillance and research. A wonderful mother, wife, daughter and friend to many, Vicki inspired us all.

read more:

Recommended composition of influenza virus vaccines for use in the 2020 Southern Hemisphere influenza season announced

(Geneva) Experts taking part in the WHO vaccine composition and information meeting (VCM) between 23-25 September 2019, organized by the WHO Global Influenza Programme, announced today the recommended components for vaccines for the 2020 Southern Hemisphere influenza season.

These recommendations are used by the national vaccine regulatory agencies and the pharmaceutical companies to develop, produce and license influenza vaccines.

read more:

GISRS - GISAID Bioinformatics Training Workshop with leading experts in Singapore

The WHO Global Influenza Programme, together with the National Centre for Infectious Diseases and the Bioinformatics Institute Singapore and the GISAID Initiative held a 2-day influenza bioinformatics workshop with hands-on sessions provided by leading experts in their respective fields, preceding the Options for the Control of Influenza X on 26-27 August 2019.

Participants trained on the GISAID EpiFlu™ database to monitor complex epidemiological relationships among circulating animal and human influenza viruses and the detection and interpretation of evolutionary change using FluSurver and Nextflu.

> GISAID Poster presented at Options X

Re-emergence of highly pathogenic avian influenza H7N9 viruses in humans in mainland China, in 2019

A severe human case of highly pathogenic avian influenza (HPAI) H7N9 occurred in late March 2019 in the Inner Mongolia autonomous region of China. The case resided near a poultry slaughtering stall, prompting immediate environmental sampling of this location.

Phylogenetic analyses of the virus showed that the sequences from the case and from several environmental samples formed a distinct clade from the gene sequences from viruses collected in 2017. Comparison with a candidate vaccine strain showed several mutations, possibly associated with antigenic drift which has yet to be characterized. No human cases of H7N9 were reported for over a year previously.

Eurosurveillance, Volume 24, Issue 21, 23/May/2019

A/Gansu/23277/2019 EPI_ISL_353991

Leading Flu Expert at US' CDC Dr. Katz says goodbye

(Atlanta) After nearly three decades at the US CDC, the Director of the WHO Collaborating Center for Surveillance, Epidemiology and Control of Influenza and Co-Chair of GISAID Scientific Advisory Council, Dr. Jackie Katz has retired. Since joining the CDC in 1992, Dr. Katz drove progress in influenza-related science and public health. She is the recipient of three Charles C. Shepard Science Awards, having co-authored over 330 peer-reviewed research articles reviews, and book chapters.

“While Dr. Katz’s leadership was most evident during the 2009 flu pandemic, her most lasting legacy may be her ability to develop young scientists through mentorship and support.” said Dr. Dan Jernigan, Director of the CDC's Influenza Division 

Prominent Influenza Researcher and Director of Japan's NIID bids farewell

(Tokyo) Dr. Takato Odagiri, Director of the Influenza Virus Research Center at the National Institute of Infectious Diseases (NIID) and Director of the WHO Collaborating Center for Reference and Research on Influenza has retired.
Dr. Odagiri began his career in 1985 as an assistant professor and a lecturer at Jichi Medical University and is the author and co-author of over 100 peer-reviewed publications.

Dr. Odagiri served on GISAID's Scientific Advisory Council since 2014, playing a critical role in providing scientific oversight of the Initiative. GISAID wishes Dr. Odagiri a healthy & happy new chapter in his life and a successful retirement. 

World Flu Day: momentum from China for influenza control

The 1st World Flu Day was formally launched at the Asian-Pacific Centenary Spanish 1918-flu symposium in Shenzhen, to raise public awareness of influenza and accelerate scientific innovation and basic research efforts particularly the development of a universal flu vaccine. Prof George Fu Gao, Director of the Chinese Center for Disease Control and Prevention and fellow researchers are pushing for stronger global political will in continuing the support of influenza prevention and control.

“2018 also marks the 15-year commemoration of the SARS outbreak, after which strengthening the CDC became the top priority in China's public policy agenda. As a result, China boosted investment in the public health system, strengthening national and local surveillance systems for all infectious diseases more efficiently and effectively, and improving research capacity, especially for emerging infectious diseases.” says Prof. Gao

> see The Lancet

Marie-Paule Kieny talks Ethics and Data Sharing at Grand Challenges 2018

Dr. Marie-Paule Kieny spoke in Berlin on October 18th at the Grand Challenges Annual Meeting, co-hosted by the Bill & Melinda Gates Foundation and the German Federal Ministry of Education & Research, discussing "Sequence data sharing – the influenza GISAID model and its wider applicability".

“In a world where global emerging disease threats demand effective sharing of information, GISAID has demonstrated what can be achieved by galvanizing the interests of public health officials, academia and industry to combat influenza” says Dr Kieny

GIHSN to share epidemiological and virological data on severe influenza via GISAID

Sanofi Pasteur’s Foundation for Influenza Epidemiology has awarded GISAID €300,000 to strengthen the Initiative and enhance its EpiFlu™ database and educational programs. In partnership with the Foundation’s Global Influenza Hospital-based Surveillance Network (GIHSN), GISAID will help promote the sharing and integration of clinical, epidemiological and virological data to better understand the impact of severe influenza and the benefit of vaccination.

“Given the high variability of influenza virus circulation, generation of comparable data across seasons with a broad geographical scope are required”, says Dr. Cédric Mahé, President of the Foundation and Head of Epidemiology at Sanofi Pasteur.

> read more

Germany's Focal Point for GISAID Karin Schwabenbauer bids farewell to official duties

Dr. Karin Schwabenbauer, Germany's Chief Veterinary Officer, a former President of the OIE World Assembly of Delegates and OIE Council, and FAO official overseeing the Animal Health Crisis Management Centre retires at the end of September. As the German Government's focal point in the GISAID Initiative, she played a key role in ensuring GISAID's recognition in FAO, OIE and WHO member states deliberations following the 2009 H1N1 pandemic.

“Karin's passion for science and unwavering commitment to improving both animal and human health made her one of the true champions of One Health. We thank Karin for her unswerving support of our Initiative, she has helped shape.” said Dr. Alan Hay, GISAID Scientific Liaison Officer

Recommended composition of influenza virus vaccines for use in the 2019 Southern Hemisphere Influenza Season announced

(Atlanta) Experts taking part in the WHO vaccine composition and information meeting (VCM) between 24-26 September, at the WHO Collaborating Centre for Surveillance, Epidemiology & Control of Influenza at the US Centers for Disease Control and Prevention (CDC), recommend components for vaccines for the 2019 Southern Hemisphere influenza season. 

read more:

GISAID announces a major contribution from Seqirus

GISAID welcomes a €250,000 donation from Seqirus, a leading innovator in influenza vaccine technologies and pandemic response solutions. Seqirus is the first influenza vaccine company to make a significant financial contribution to GISAID.

“Seqirus is proud to support GISAID in its mission to provide open and rapid access to influenza virus data for the public health good of all nations,” said Gordon Naylor, President of Seqirus

> read more

Renowned scientist and public health specialist to advise the GISAID Initiative on international affairs

Dr. Marie-Paule Kieny, a former Assistant Director-General of WHO will advise GISAID on international affairs. Most recently Dr Kieny led the WHO research & development initiative during the Ebola crisis resulting in the WHO R&D Blueprint for public health emergencies, with an emphasis on enhanced global collaboration and timely sample and data sharing to support rapid emergency response.

“In a world where global emerging disease threats demand effective sharing of information, GISAID has demonstrated what can be achieved by galvanizing the interests of public health officials, academia and industry to combat influenza” said Dr. Kieny

Celebrating 70 Years GIP and 65 Years Global Influenza Surveillance and Response System

GISAID salutes GIP and GISRS. It was 1947 when the WHO’s Interim Committee recognized the importance of Influenza and started a globally-coordinated effort for its surveillance, study and control that saw the beginning of the Global Influenza Programme. By 1952, the WHO Executive Board called for an influenza surveillance system to collect, correlate and distribute information regarding occurrence, epidemiology and laboratory findings. Today GISRS encompasses 143 institutions across 113 Member States. A global disease surveillance network built on voluntary collaboration and real-time reporting that makes up the backbone of today's global influenza surveillance.  

Science Editorial: Can we beat influenza?

G20 Health Ministers recognize the importance of GISAID in regard to virus data sharing

At the invitation of Germany, the first meeting of Health Ministers of the Group of Twenty leading industrialized and emerging economies (G20) took place in Berlin between 19-20 May 2017.

Under the banner of “Together Today for a Healthy Tomorrow – Joint Commitment for Shaping Global Health”, the two-day meeting focused on combating global health hazards. In their Berlin Declaration, the G20 Health Ministers recognize the importance of the Global Initiative on Sharing All Influenza Data (GISAID).

> read more
> The Berlin Declaration of the G20 Health Ministers (2017)

Sharing of Ebola data needs good practice framework, what GISAID did for influenza

The rapid dissemination of results during outbreaks is sporadic at best. In the case of influenza, a global initiative called GISAID established a framework for good practice. Largely thanks to this, during the 2009 H1N1 influenza outbreak, it became a go-to place for the community to deposit and locate H1N1 sequence information.

Pardis C. Sabeti et al, Nature 518, 477–479 (26 February 2015)

> Read the commentary
> WHO Ebola Situation Report