GISAID: Global initiative on sharing all influenza data - from vision to reality.
30 Mar 2017-Eurosurveillance (European Centre for Disease Prevention and Control)-Vol. 22, Iss: 13, pp 30494
TL;DR: This poster presents a poster presenting a poster presented at the 2016 International Conference of the Association for the Study of Viral Influenza and its Disruption in China, where it was presented for the first time.
Abstract: Yuelong Shu1, John McCauley2 1. WHO Collaborating Center for Reference and Research on Influenza, Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China 2. WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, the Francis Crick Institute, London, United Kingdom
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TL;DR: This case highlights the importance of close coordination between clinicians and public health authorities at the local, state, and federal levels, as well as the need for rapid dissemination of clinical information related to the care of patients with this emerging infection.
Abstract: An outbreak of novel coronavirus (2019-nCoV) that began in Wuhan, China, has spread rapidly, with cases now confirmed in multiple countries. We report the first case of 2019-nCoV infection confirmed in the United States and describe the identification, diagnosis, clinical course, and management of the case, including the patient's initial mild symptoms at presentation with progression to pneumonia on day 9 of illness. This case highlights the importance of close coordination between clinicians and public health authorities at the local, state, and federal levels, as well as the need for rapid dissemination of clinical information related to the care of patients with this emerging infection.
4,970 citations
TL;DR: A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic, and it is found that the G614 variant grows to higher titer as pseudotyped virions.
3,302 citations
Cites methods from "GISAID: Global initiative on sharin..."
...Data Pipeline Background and General Approach The Global Initiative for Sharing All Influenza Data (GISAID) (Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017) has been coordinating SARS-CoV-2 genome sequence submissions and making data available for download since early in the pandemic....
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...Phylogenetic analysis of the global sampling of SARS-CoV-2 is being very capably addressed by the Global Initiative for Sharing All Influenza Data (GISAID) database (https://www.gisaid.org/; Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017) and Nextstrain (https:// nextstrain....
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TL;DR: A rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread and is designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide.
Abstract: The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of SARS-CoV-2. Here, we present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. Our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and delabelling virus lineages that become unobserved and hence are probably inactive. By focusing on active virus lineages and those spreading to new locations, this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of SARS-CoV-2.
2,093 citations
TL;DR: A review of the literature on mutations of the SARS-CoV-2 spike protein, the primary antigen, focusing on their impacts on antigenicity and contextualizing them in the protein structure is presented in this article.
Abstract: Although most mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome are expected to be either deleterious and swiftly purged or relatively neutral, a small proportion will affect functional properties and may alter infectivity, disease severity or interactions with host immunity. The emergence of SARS-CoV-2 in late 2019 was followed by a period of relative evolutionary stasis lasting about 11 months. Since late 2020, however, SARS-CoV-2 evolution has been characterized by the emergence of sets of mutations, in the context of ‘variants of concern’, that impact virus characteristics, including transmissibility and antigenicity, probably in response to the changing immune profile of the human population. There is emerging evidence of reduced neutralization of some SARS-CoV-2 variants by postvaccination serum; however, a greater understanding of correlates of protection is required to evaluate how this may impact vaccine effectiveness. Nonetheless, manufacturers are preparing platforms for a possible update of vaccine sequences, and it is crucial that surveillance of genetic and antigenic changes in the global virus population is done alongside experiments to elucidate the phenotypic impacts of mutations. In this Review, we summarize the literature on mutations of the SARS-CoV-2 spike protein, the primary antigen, focusing on their impacts on antigenicity and contextualizing them in the protein structure, and discuss them in the context of observed mutation frequencies in global sequence datasets. The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been characterized by the emergence of mutations and so-called variants of concern that impact virus characteristics, including transmissibility and antigenicity. In this Review, members of the COVID-19 Genomics UK (COG-UK) Consortium and colleagues summarize mutations of the SARS-CoV-2 spike protein, focusing on their impacts on antigenicity and contextualizing them in the protein structure, and discuss them in the context of observed mutation frequencies in global sequence datasets.
2,047 citations
TL;DR: The current outbreak of the novel coronavirus Covid-19 (coronavirus disease 2019; previously 2019-nCoV), epi-centered in Hubei Province of the People's Republic of China, has spread to many other countries and the incidence in other Asian countries, in Europe and North America remains low so far.
Abstract: The current outbreak of the novel coronavirus Covid-19 (coronavirus disease 2019; previously 2019-nCoV), epi-centered in Hubei Province of the People's Republic of China, has spread to many other countries. On January 30, 2020, the WHO Emergency Committee declared a global health emergency based on growing case notification rates at Chinese and international locations. The case detection rate is changing hourly and daily and can be tracked in almost real time on website provided by Johns Hopkins University [1] and other websites. As of early February 2020, China bears the large burden of morbidity and mortality, whereas the incidence in other Asian countries, in Europe and North America remains low so far.
1,940 citations
References
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TL;DR: Novel reassortant H7N9 viruses were associated with severe and fatal respiratory disease in three patients, and all three patients died.
Abstract: Background Infection of poultry with influenza A subtype H7 viruses occurs worldwide, but the introduction of this subtype to humans in Asia has not been observed previously. In March 2013, three urban residents of Shanghai or Anhui, China, presented with rapidly progressing lower respiratory tract infections and were found to be infected with a novel reassortant avian-origin influenza A (H7N9) virus. Methods We obtained and analyzed clinical, epidemiologic, and virologic data from these patients. Respiratory specimens were tested for influenza and other respiratory viruses by means of real-time reverse-transcriptase–polymerase-chain-reaction assays, viral culturing, and sequence analyses. Results A novel reassortant avian-origin influenza A (H7N9) virus was isolated from respiratory specimens obtained from all three patients and was identified as H7N9. Sequencing analyses revealed that all the genes from these three viruses were of avian origin, with six internal genes from avian influenza A (H9N2) virus...
2,113 citations
"GISAID: Global initiative on sharin..." refers background in this paper
...WHO Collaborating Center for Reference and Research on Influenza, Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China 2....
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...Acceptance of the GISAID sharing mechanism by providers and users of data, and the confidence of the influenza community, were further illustrated in 2013 by the unprecedented immediate release of the genetic sequences of Influenza A(H7N9) viruses from the first human cases, by Chinese scientists at the WHO Collaborating Centre for Influenza in Beijing [11,12]....
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10 Jan 2017
TL;DR: The article finds that the Global Initiative on Sharing All Influenza Data contributes to global health in at least five ways: collating the most complete repository of high‐quality influenza data in the world; facilitating the rapid sharing of potentially pandemic virus information during recent outbreaks; supporting the World Health Organization's biannual seasonal flu vaccine strain selection process; developing informal mechanisms for conflict resolution around the sharing of virus data.
Abstract: The international sharing of virus data is critical for protecting populations against le-thal infectious disease outbreaks. Scientists must rapidly share information to assessthe nature of the threat and develop new medical countermeasures. Governmentsneed the data to trace the extent of the outbreak, initiate public health responses,and coordinate access to medicines and vaccines. Recent outbreaks suggest, however,that the sharing of such data cannot be taken for granted – making the timely inter-national exchange of virus data a vital global challenge. This article undertakes thefirst analysis of the Global Initiative on Sharing All Influenza Data as an innovativepolicy effort to promote the international sharing of genetic and associated influenzavirus data. Based on more than 20 semi-structured interviews conducted with key in-formants in the international community, coupled with analysis of a wide range ofprimary and secondary sources, the article finds that the Global Initiative on SharingAll Influenza Data contributes to global health in at least five ways: (1) collating themost complete repository of high-quality influenza data in the world; (2) facilitatingthe rapid sharing of potentially pandemic virus information during recent outbreaks;(3) supporting the World Health Organization’s biannual seasonal flu vaccine strainselection process; (4) developing informal mechanisms for conflict resolution aroundthe sharing of virus data; and (5) building greater trust with several countries key toglobal pandemic preparedness.
1,570 citations
"GISAID: Global initiative on sharin..." refers background in this paper
...Today GISAID is recognised as an effective and trusted mechanism for rapid sharing of both published and ‘unpublished’ influenza data [4]....
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University of Birmingham1, Bernhard Nocht Institute for Tropical Medicine2, University of Toronto3, Ontario Institute for Cancer Research4, European Centre for Disease Prevention and Control5, Public Health England6, University of Edinburgh7, Robert Koch Institute8, Swiss Tropical and Public Health Institute9, University College London10, Paul Ehrlich Institute11, University of Liverpool12, Rega Institute for Medical Research13, Kenya Medical Research Institute14, Friedrich Loeffler Institute15, Janssen-Cilag16, Technische Universität München17, Public Health Agency of Canada18, Pasteur Institute19, Sandia National Laboratories20, MRIGlobal21, World Health Organization22, University of London23, Norwegian Institute of Public Health24, Defence Science and Technology Laboratory25, Bundeswehr Institute of Microbiology26, National Institutes of Health27
TL;DR: This paper presents sequence data and analysis of 142 EBOV samples collected during the period March to October 2015 and shows that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.
Abstract: A nanopore DNA sequencer is used for real-time genomic surveillance of the Ebola virus epidemic in the field in Guinea; the authors demonstrate that it is possible to pack a genomic surveillance laboratory in a suitcase and transport it to the field for on-site virus sequencing, generating results within 24 hours of sample collection. This paper reports the use of nanopore DNA sequencers (known as MinIONs) for real-time genomic surveillance of the Ebola virus epidemic, in the field in Guinea. The authors demonstrate that it is possible to pack a genomic surveillance laboratory in a suitcase and transport it to the field for on-site virus sequencing, generating results within 24 hours of sample collection. The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths1. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10−3 and 1.42 × 10−3 mutations per site per year. This is equivalent to 16–27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic2,3,4,5,6,7. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions8. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities9. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15–60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.
1,187 citations
"GISAID: Global initiative on sharin..." refers background in this paper
...Such a trusted system could complement and take full advantage of the latest advances in rapid sequencing of specimens in the laboratory and in the field, for outbreak investigation [24]....
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TL;DR: It is shown that long-distance migratory birds can play a major role in the global spread of avian influenza viruses and that the H5N8 virus that recently caused serious outbreaks in European and North American poultry farms came from migrant ducks, swans, and geese that meet at their Arctic breeding grounds.
Abstract: Avian influenza viruses affect both poultry production and public health. A subtype H5N8 (clade 2.3.4.4) virus, following an outbreak in poultry in South Korea in January 2014, rapidly spread worldwide in 2014-2015. Our analysis of H5N8 viral sequences, epidemiological investigations, waterfowl migration, and poultry trade showed that long-distance migratory birds can play a major role in the global spread of avian influenza viruses. Further, we found that the hemagglutinin of clade 2.3.4.4 virus was remarkably promiscuous, creating reassortants with multiple neuraminidase subtypes. Improving our understanding of the circumpolar circulation of avian influenza viruses in migratory waterfowl will help to provide early warning of threats from avian influenza to poultry, and potentially human, health.
326 citations
Chinese Academy of Sciences1, Chinese Center for Disease Control and Prevention2, Jilin University3, Centers for Disease Control and Prevention4, Center for Veterinary Medicine5, Novosibirsk State University6, South China Agricultural University7, Tsinghua University8, Guangxi University9, Broad Institute10
TL;DR: Phylogenetic analysis reveals that H5N6 arose from reassortments of H5 and H6N6 viruses, with the hemagglutinin and neuraminidase combinations being strongly lineage specific.
235 citations
"GISAID: Global initiative on sharin..." refers background in this paper
...GISAID’s ability to facilitate efficient global collaborations, such as the Global Consortium for H5N8 and Related Influenza Viruses [16,17], is central to monitoring phylogeographic interrelationships among, for example, H5 subtype viruses in wild and domestic birds in relation to their incidence, cross-border spread and veterinary impact, and assessing risk to animal and human health [18]....
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