DOCSLIB.ORG

Genomics and Epidemiological Surveillance Stephanie W

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genomics and Epidemiological Surveillance Stephanie W NEWS & ANALYSIS GENOME WATCH Genomics and epidemiological surveillance Stephanie W. Lo and Dorota Jamrozy This month’s Genome Watch highlights viral transmission, identify viral mutations D614 vari ant, which might be indicative of how genomic surveillance can provide and integrate viral data with health data2. By potential positive selection. The viral genome important information for identifying June 2020, the consortium sequenced >20,000 data were linked with patient clinical infor- and tracking emerging pathogens such SARS- CoV-2 genomes and defined transmis- mation, which showed that the G614 variant as SARS- CoV-2. sion lineages based on phylogeny. Open data might be associated with potentially higher sharing and standardized lineage definitions viral loads but not with disease severity. The timely detection and surveillance of infec- (Global Initiative on Sharing All Influenza Updated data and current global counts of tious diseases and responses to pandemics Data (GISAID)) were established to enable the spike 614 variants are available in the are crucial but challenging. Whole-genome global efforts in detecting emerging lineages COVID-19 Viral Genome Analysis Pipeline. sequencing (WGS) is a common tool for path- and mutations that are relevant for outbreak Genomic surveillance can generate a rich ogen identification and tracking, establishing control and vaccine development on an inter- source of information for tracking pathogen transmission routes and outbreak control. national level3. By the end of June 2020, >57,000 transmission and evolution on both national At the turn of 2019/20, Wu et al1 used SARS- CoV-2 genomes from around 100 dif- and international levels. More importantly, metagenomic RNA sequencing to identify the ferent countries have been deposited in the the recent application of genomics in surveil- aetiology of an at this point unknown respira- GISAID database. To overcome the challenge in lance of COVID-19 highlighted its useful- tory disease in a single patient in Wuhan, China, data analysis and interpretation, user-friendly ness in the nearly real-time response to a public where several cases of severe respir atory infec- web- based applications were designed for lin- health crisis. tions have been reported. The authors identi- age assignment (Pangolin COVID-19 Lineage Stephanie W. Lo ✉ and Dorota Jamrozy ✉ fied the potential causative pathogen as a new Assigner) and to interactively visualize the cir- Parasites and Microbes, Wellcome Sanger Institute, coronavirus by reconstructing the viral genome culating lineages on national and international Wellcome Genome Campus, Hinxton, UK. from the bronchoal veolar lavage fluid sample scales (for example, Microreact and Nextstrain). ✉e- mail: [email protected] of the patient. In early January 2020, the viral The international effort towards open data https://doi.org/10.1038/s41579-020-0421-0 genome sequence was released, which facilitated sharing is of major scientific benefit, enabling 1. Wu, F. et al. A new coronavirus associated with human the development of rapid molecular diagnos- monitoring of SARS-CoV-2 evolution in nearly respiratory disease in China. Nature 579, 265–269 (2020). 4 tics assays worldwide. Subsequently, the virus real time and on a global level. Korber et al. 2. The COVID-19 Genomics UK (COG- UK) consortium. (now known as SARS-CoV-2, which causes the developed a bioinformatics pipeline to track An integrated national scale SARS- CoV-2 genomic surveillance network. Lancet Microbe 1, e99–e100 ongoing coronavirus disease 2019 (COVID-19) changes in the SARS-CoV-2 spike glyco protein, (2020). pandemic) rapidly spread globally, and there which mediates host cell entry and is a key 3. Rambaut, A. et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic has been an immediate effort to study viral vaccine target. The pipeline monitors changes epidemiology. Nat. Microbiol. https://doi.org/10.1038/ transmission and evolution in the amino acid sequence of spike over time to s41564-020-0770-5 (2020). 4. Korber, B. et al. Tracking changes in SARS- CoV-2 using WGS. For example, identify variants that are concomitantly Spike: evidence that D614G increases infectivity SARS-CoV-2 Sequen- increasing in frequency in differ- of the COVID-19 virus. Cell https://doi.org/10.1016/ j.cell.2020.06.043 (2020). cing for Public Health ent geographic locations. The Competing interests Emergency Response, analysis, which was enabled The authors declare no competing interests. Epidemiology and Sur- by data from GISAID, sug- veillance (SPHERES) in gested that a SARS- CoV-2 RELATED LINKS the United States and the variant carrying a particu- COG- UK: https://www.cogconsortium.uk COVID-19 Viral Genome Analysis pipeline: https://cov.lanl. 2 COVID-19 Genomics UK lar spike mutation (D614G) gov/content/index (COG- UK) in the United became globally dominant GISAID: https://www.gisaid.org/ Microreact: https://microreact.org/showcase Kingdom. over a period of one month. Nextstrain: https://nextstrain.org Phylogenetic Assignment of Named Global Outbreak The latter consortium C Comparison of different re LINeages COVID-19 Lineage Assigner: https://pangolin. d d was launched in March 2020 i te regions revealed consistent t: i cog- uk.io/ P im hil L SPHERES: https://www.cdc.gov/coronavirus/2019- ncov/ as a nationwide genomic surveil- ip ure patterns of the G614 vari ant Pat at covid- data/spheres.html lance network that aims to track enall/Springer N replacing a previously established 478 | SEPTEMBER 2020 | VOLUME 18 ww w. na tu re .c om /n rm icro.
Load more

Recommended publications
  • COVID-19 Vaccines, Cases and Variants
    COVID-19 Critical Intelligence Unit: COVID-19 vaccines, cases and variants COVID-19 Monitor COVID-19 vaccines, cases and variants 24 June 2021 Background • Despite large numbers of vaccinations following the initial vaccine rollout, the United States, India, Chile and Europe have had a surge in COVID-19 cases. It is suspected that relaxation of public health measures, as well as the new variants of COVID-19, may have contributed to this. New variants may be more transmissible and less susceptible to antibodies produced by vaccines or previous infection.(1-6) • While preliminary research from Israel suggests that vaccination reduces transmission, vaccination alone is insufficient to contain COVID-19.(7, 8) Evidence • Viruses constantly change through mutation and, over time, new variants of a virus are expected to occur. Some variants have characteristics that have a significant impact on transmissibility, severity of disease and the effectiveness of vaccines.(9) • For SARS-CoV-2, there are currently four variants of concern as determined by the World Health Organization (WHO).(10) The WHO has recently assigned simple labels for key variants of SARS- CoV-2, included below.(11) • The four variants of concern include: o Alpha (B.1.1.7), which originated in the United Kingdom. Currently 136 countries are reporting detection of the variant. o Beta (B.1.351), which originated in South Africa. Currently 92 countries are reporting detection of the variant. o Gamma (B.1.1.28.1 or P.1), which originated in Brazil. Currently 54 countries are reporting detection of the variant. o Delta (B.1.617.2), which originated in India.
    [Show full text]
  • SARS-Cov-2 Variants ACKNOWLEDGEMENTS
    SARS-CoV-2 variants ACKNOWLEDGEMENTS This report was developed by PHG Foundation for FIND (the Foundation for Innovative New Diagnostics). The work was supported by Unitaid and UK aid from the British people. We would like to thank all those who contributed to the development and review of this report. Lead writers Chantal Babb de Villiers (PHG Foundation) Laura Blackburn (PHG Foundation) Sarah Cook (PHG Foundation) Joanna Janus (PHG Foundation) Reviewers Devy Emperador (FIND) Jilian Sacks (FIND) Marva Seifert (FIND/UCSD) Anita Suresh (FIND) Swapna Uplekar (FIND) Publication date: 11 March 2021 URLs correct as of 4 March 2021 SARS-CoV-2 variants CONTENTS 1 Introduction ............................................................................................................................ 3 2 SARS-CoV-2 variants and mutations .................................................................................... 3 2.1 Definitions of variants of concern ...................................................................................... 4 2.2 Initial variants of concern identified ................................................................................... 5 2.3 Variants of interest ............................................................................................................ 7 3 Impact of variants on diagnostics ........................................................................................ 7 3.1 Impact of variants of concern on diagnostics ...................................................................
    [Show full text]
  • WHO Survey on the Sharing of Genetic Sequence Data Of
    WHO Survey on the Sharing of Genetic Sequence Data of Influenza Viruses with Human Pandemic Potential Results and Analysis of data received 27 April 2016 Table of Contents Acknowledgement .................................................................................................................................. 3 Acronyms ................................................................................................................................................ 4 Executive Summary ................................................................................................................................. 5 Background ............................................................................................................................................. 8 Methodology Summary .......................................................................................................................... 9 IVPP GSD Sharing in Numbers (as of October 2014)............................................................................. 10 Survey Results ....................................................................................................................................... 11 1. Mechanisms for sharing of IVPP GSD........................................................................................ 11 2. Ease of sharing .......................................................................................................................... 13 3. Systematic sharing ...................................................................................................................
    [Show full text]
  • Avian Influenza A(H10N7) Virus–Associated Mass Deaths Among Harbor Seals
    Article DOI: http://dx.doi.org/10.3201/eid2104.141675 Avian Influenza A(H10N7) Virus–Associated Mass Deaths among Harbor Seals Technical Appendix Technical Appendix Table. Details of hemagglutinin sequences shown in the Figure* Isolate name Accession no. Online database A/seal/Germany/EMC-1/2014(H10N7) EPI544351 GISAID EpiFlu A/mallard/Netherlands/1/2014(H10N7) EPI552751 GISAID EpiFlu A/mallard/Sweden/133546/2011(H10N4) CY183991.1 GenBank A/domestic duck/RepublicofGeorgia/2/2010(H10N7) CY185457.1 GenBank A/domestic duck/RepublicofGeorgia/1/2010(H10(N7) CY185449.1 GenBank A/mallard/Sweden/104746/2009(H10N1) CY183855.1 GenBank A/mallard/Sweden/105465/2009(H10N1) CY183927.1 GenBank A/mallard/Sweden/102260/2009(H10N1) CY183847.1 GenBank A/mallard/Sweden/105323/2009(H10N1) CY183887.1 GenBank A/mallard/Sweden/105402/2009(H10N1) CY183911.1 GenBank A/mallard/Sweden/105522/2009(H10N1) JX566079.1 GenBank A/mallard/Netherlands/50/2010(H10N7) EPI552752 GISAID EpiFlu A/mallard/Netherlands/47/2010(H10N7) EPI552753 GISAID EpiFlu A/mallard/Republic of Georgia/14/2011(H10N7) CY185689.1 GenBank A/mallard/Republic of Georgia/15/2011(H10N7) CY185385.1 GenBank A/northern pintail/Egypt/EMC-1/2012(H10N7) EPI552754 GISAID EpiFlu A/mallard/Egypt/EMC-4/2012(H10N7) EPI552755 GISAID EpiFlu A/mallard/Netherlands/1/2012(H10N7) EPI552756 GISAID EpiFlu A/shoveler/Egypt/01198-NAMRU3/2007(H10N7) EPI372402† GISAID EpiFlu A/Jiangxi-Donghu/346/2013(H10N8) EPI497477‡ GISAID EpiFlu A/chicken/Jiangxi/102/2013(H10N8) EPI530542§ GISAID EpiFlu *We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) EpiFluTM database on which this research is based.
    [Show full text]
  • Investigation of Novel SARS-Cov-2 Variant
    SARS-CoV-2 variant data update, England Version 10 6 August 2021 This briefing provides an update on previous data located in technical and variant data update briefings and updates up to 23 July 2021. 1 Investigation of SARS-CoV-2 Variants of Concern. Version 10. Contents Contents .............................................................................................................................. 2 Data on individual variants .................................................................................................. 5 Alpha ............................................................................................................................... 5 Beta ................................................................................................................................. 9 Gamma .......................................................................................................................... 13 Zeta ............................................................................................................................... 17 Eta ................................................................................................................................. 20 VUI-21FEB-04 (B.1.1.318) ............................................................................................ 23 Theta ............................................................................................................................. 26 Kappa ...........................................................................................................................
    [Show full text]
  • APHL SARS-Cov-2 Sequencing Recommendations
    Recommendations for SARS-CoV-2 Sequence Data Quality & Reporting Version 1 • March 1, 2021 www.aphl.org Introduction Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), emerged in late 2019 in Wuhan, China.1 Since being identified, SARS-CoV-2 has spread across the globe resulting in over 113 million cases of COVID-19 and 2.5 million deaths.2 In the US, public health laboratories have played a critical role in the response to the COVID-19 pandemic. As the availability of molecular and serologic/antibody based testing diagnostics has expanded, so too has the work performed by public health laboratories. Currently, efforts are underway to improve the coordination of genomic sequencing of SARS-CoV-2 in the US. Next generation sequencing (NGS) is a tool commonly used in public health surveillance and outbreak response. There are currently multiple efforts in public and private sectors to sequence SARS-CoV-2 genomes, but they are not yet well coordinated. This includes increasing the amount of sequencing performed in state and local public health laboratories. Currently, laboratories are using different sequencing strategies and protocols, including but not limited to differences in sample selection, library preparation and sequencing platforms, bioinformatics workflows, and data interpretation, which are leading to inconsistent data quality standards and biases among SARS-CoV-2 sequences generated by public health laboratories in public databases. While these issues are not unique to public health laboratories, providing basic guidance on SARS-CoV-2 sequencing and data sharing practices will improve coordination of laboratories that have been conducting sequencing and provide expectations for public health laboratories that are currently building capacity.
    [Show full text]
  • Outbreak of SARS Cov 2 B.1.1.7 Lineage After Vaccination in German Long Term Care
    Outbreak of SARS-CoV-2 B.1.1.7 Lineage after Vaccination in Long-Term Care Facility, Germany, February–March 2021 Pinkus Tober-Lau,1 Tatjana Schwarz,1 David Hillus, Jana Spieckermann, Elisa T. Helbig, Lena J. Lippert, Charlotte Thibeault, Willi Koch, Leon Bergfeld, Daniela Niemeyer, Barbara Mühlemann, Claudia Conrad, Stefanie Kasper, Friederike Münn, Frank Kunitz, Terry C. Jones, Norbert Suttorp, Christian Drosten, Leif Erik Sander,2 Florian Kurth,2 Victor M. Corman2 One week after second vaccinations were administered, fi rst week after the second dose (3). Although break- an outbreak of B.1.1.7 lineage severe acute respiratory through infections have been reported, vaccinated syndrome coronavirus 2 infections occurred in a long- persons were at substantially lower risk for infection term care facility in Berlin, Germany, aff ecting 16/20 vac- and symptomatic disease (4,5). cinated and 4/4 unvaccinated residents. Despite consid- The variant of concern (VOC) B.1.1.7 rapidly erable viral loads, vaccinated residents experienced mild became the predominant lineage in Europe in 2021. symptoms and faster time to negative test results. Analyses estimated that B.1.1.7 has increased trans- missibility and a <0.7 higher reproduction number utbreaks of severe acute respiratory syndrome (6). Neutralization activity of serum samples from Ocoronavirus 2 (SARS-CoV-2) in long-term care BNT162b2-vaccinated persons has been shown to facilities (LTCF) are of great concern and have been be slightly reduced against B.1.1.7 in cell culture (7), reported to have high case-fatality rates (1). Conse- but observational data from Israel suggest BNT162b2 quently, national vaccination strategies prioritize res- vaccination is effective against B.1.1.7 (8).
    [Show full text]
  • Press Release
    PRESS RELEASE GISAID announces a major contribution from Seqirus to support open and rapid sharing of influenza virus data Munich, Germany - 26 July 2018 – The Global Initiative on Sharing All Influenza Data (GISAID), a non-profit organization and public-private partnership dedicated to strengthening the world’s defense against deadly influenza threats, today welcomed a €250,000 donation from Seqirus, a leading innovator in influenza vaccine technologies and pandemic response solutions. GISAID is recognized as the world’s foremost global collaboration of scientists and governments, from developed and developing countries, to promote the near-real time exchange and analysis of data on the ever-changing influenza viruses that threaten global populations. It has brought together 8,000 scientists from 1,000 institutions around the world to create the largest and most up-to-date publicly-accessible collection of genetic data on influenza viruses. This initial contribution from Seqirus is the first of its kind from the influenza vaccine industry and will bolster GISAID’s efforts to advance bioinformatics and the interpretation of influenza data. The donation will be used to enhance GISAID’s database, to fund education programmes that aim to strengthen understanding of the impact of influenza and to support general operations. “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. “The GISAID platform plays a crucial role in the timely identification of changes in the viruses to reduce response times and mitigate the impact of seasonal and pandemic influenza.” “The centenary year of the 1918 pandemic presents an opportune moment to reflect on progress made against the threat of pandemic influenza,” said Peter Bogner, President of GISAID.
    [Show full text]
  • SARS-Cov-2 Variant Analysis Henrik Torres1, Amith Vasantha2, Helen Chow3, Gepoliano Chaves Phd4
    SARS-CoV-2 Variant Analysis Henrik Torres1, Amith Vasantha2, Helen Chow3, Gepoliano Chaves PhD4 1Choate Rosemary Hall, 333 Christrian Street, Wallingford, CT 06492 2Basis Independent Silicon Valley, 1290 Parkmoor Ave, San Jose, CA 95126 3Lowell High School, 1101 Eucalyptus Dr, San Francisco, CA 94132 4University of Chicago, 5801 S Ellis Ave, Chicago, IL 60637 Abstract— The SARS-CoV-2 virus started the novel II. METHODS coronavirus pandemic. SARS-CoV-2 is an RNA virus that causes infection through the binding of the virion’s spike protein to a Data was collected from the NCBI SRA Database and the cell’s ACE2 receptor. The SARS-CoV-2 virion cleaves its way GISAID Database in the form of FASTQ files and FASTA into the cell and deposits its RNA genome that hijacks the cell’s files, respectively. FASTQ files and FASTA files both RNA replication system to produce more virions. During function to store genomic information, with the important replication, genetic variance arises through single nucleotide polymorphisms (SNPs) that can enable a zoonotic jump or affect distinction being that FASTA files store a nucleotide the transmissibility or lethality of a virus [3]. Our research sequence, while FASTQ files add quality scores to each focused on studying these SNPs from collected FASTQ and nucleotide. Several FASTQ and FASTA files were collected FASTA files of human, pangolin, and bat SARS-CoV-2 genomes from NCBI and GISAID with each continent except on online databases such as the NCBI SRA Browser and GISAID Antarctica being equally represented. To analyze the FASTQ and running files through variant call pipelines.
    [Show full text]
  • COVID-19 Genomic Surveillance Regional Network
    COVID-19 Genomic Surveillance Regional Network Dr. Juliana Leite LaboratorySpecialist, Viral Disease Infectious Hazard Management (IHM) PAHO Health Emergencies Department (PHE) Virtual meeting 28 - 30 October 2019 OPS/OMS COVID-19 Genomic Surveillance Regional Network Latin America Region Laboratory • Implementation of a Response Capacity SARS-CoV-2 genomic Caribbean Regian surveillance network in the Americas region Pan American Health Organization OPS/OMS BACKGROUND The response to Emerging Infectious Diseases Regardless of geographic location, an outbreak or epidemic represents an emergency and a potential international threat. There are no countries or institutions that have the complete PRINCIPLES capacity to respond by themselves to epidemics, especially those generated by new (emerging) pathogens with pandemic potential. For this reason, a system is required that coordinates alert and response mechanisms at the global and regional levels. OPS/OMS BACKGROUND The response to Emerging Infectious Diseases Beyond surveillance of endemic pathogens, WHO Member States should be prepared to detect and characterize in a timely manner the emergence of new agents with epidemic potential* Mechanisms for a timely access to National and Regional reference laboratories as well as laboratory networks, must be granted *Core capacity #8 IHR Quality of the results should be ensured OPS/OMS BACKGROUND The response to COVID-19 pandemic Firsts genomic sequences C harité Protocol released in open platform Primers and Probes (Virological and GISAID) Ordering
    [Show full text]
  • First Detection of SARS-Cov-2 B.1.1.7 Variant of Concern in an Asymptomatic Dog in Spain
    viruses Case Report First Detection of SARS-CoV-2 B.1.1.7 Variant of Concern in an Asymptomatic Dog in Spain Sandra Barroso-Arévalo 1,2,* , Belén Rivera 1,2, Lucas Domínguez 1,2 and José M. Sánchez-Vizcaíno 1,2 1 VISAVET Health Surveillance Center, Animal Health Department, Complutense University of Madrid, 28040 Madrid, Spain; [email protected] (B.R.); [email protected] (L.D.); [email protected] (J.M.S.-V.) 2 Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, 28040 Madrid, Spain * Correspondence: [email protected] Abstract: Natural SARS-CoV-2 infection in pets has been widely documented during the last year. Although the majority of reports suggested that dogs’ susceptibility to the infection is low, little is known about viral pathogenicity and transmissibility in the case of variants of concern, such as B.1.1.7 in this species. Here, as part of a large-scale study on SARS-CoV-2 prevalence in pets in Spain, we have detected the B.1.1.7 variant of concern (VOC) in a dog whose owners were infected with SARS-CoV-2. The animal did not present any symptoms, but viral loads were high in the nasal and rectal swabs. In addition, viral isolation was possible from both swabs, demonstrating that the dog was shedding infectious virus. Seroconversion occurred 23 days after the first sampling. This study documents the first detection of B.1.1.7 VOC in a dog in Spain and emphasizes the importance of performing active surveillance and genomic investigation on infected animals.
    [Show full text]
  • Towards Fair and Sustainable Real-Time Sharing of Data During Emergencies
    Towards fair and sustainable real-time sharing of data during emergencies Sequence data sharing through GISAID A move to open science for COVID-19 vaccine trials in France Marie-Paule Kieny Inserm, France Experience during SARS, H1N1 influenza pandemic and Ebola • Data sharing was slow and inconsistent • Some samples were exported without proper Material Transfer agreement • Concerns about ownership • Concerns about Intellectual Property Rights • Concerns about possibility to publish data already publicly released • Lack of trust • Others… Data/information sharing during outbreaks/ epidemics: what is needed? • Epidemiological • Surveillance (clinical, laboratory) • Emergency response • Health facility data • Research data including surveys, observational studies, clinical trials of diagnostics, therapeutics and preventives • QC’d interim results • Final research results • Ancillary research results • ‘Negative’ and inconclusive results 3 Genomic sequence data Development of the GISAID data sharing principles • GISAID sharing agreement developed with WHO MS Support (DAA) as a response to many countries refusing to share sequence data • Open Access Data sharing platform since 2008 • Essential for the Global Influenza Surveillance and Response System (GISRS) • Real-time progress in the understanding of the new COVID-19 disease and in the research and development of candidate medical countermeasures • March 2020: o 2,500 institutions entrust data to GISAID o 34,000 participating researchers Publicly-accessible data during the COVID-19 Pandemic
    [Show full text]