Global landscape of SARS-CoV-2 genomic surveillance and data sharing

[1]  J. Bybjerg-Grauholm,et al.  Epidemiological characterisation of the first 785 SARS-CoV-2 Omicron variant cases in Denmark, December 2021 , 2021, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[2]  E. Callaway.  Heavily mutated Omicron variant puts scientists on alert , 2021, Nature.

[3]  R. Adegbola,et al.  SARS-CoV-2 sequencing collaboration in west Africa shows best practices , 2021, The Lancet Global Health.

[4]  C. Whittaker,et al.  Under-reporting of deaths limits our understanding of true burden of covid-19 , 2021, BMJ.

[5]  M. Koopmans,et al.  Supplementing SARS-CoV-2 genomic surveillance with PCR-based variant detection for real-time actionable information, the Netherlands, June to July 2021 , 2021, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[6]  M. Baguelin,et al.  Non-pharmaceutical interventions, vaccination, and the SARS-CoV-2 delta variant in England: a mathematical modelling study , 2021, The Lancet.

[7]  A. Dopazo,et al.  The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant , 2021, Nature Genetics.

[8]  M. Koopmans,et al.  The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology , 2021, Nature Medicine.

[9]  D. DeMets,et al.  Genomic surveillance to combat COVID-19: challenges and opportunities , 2021, The Lancet Microbe.

[10]  A. Azman,et al.  Neutralizing antibodies against SARS-CoV-2 variants induced by natural infection or vaccination: a systematic review and pooled meta-analysis. , 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[11]  O. Pybus,et al.  Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool , 2021, Virus evolution.

[12]  Scott M. Williams,et al.  Global variation in sequencing impedes SARS-CoV-2 surveillance , 2021, PLoS genetics.

[13]  C. Swanton,et al.  AZD1222-induced neutralising antibody activity against SARS-CoV-2 Delta VOC , 2021, The Lancet.

[14]  P. Kaleebu,et al.  Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda , 2021, Nature Microbiology.

[15]  M. Biggerstaff,et al.  Genomic Surveillance for SARS-CoV-2 Variants Circulating in the United States, December 2020–May 2021 , 2021, MMWR. Morbidity and mortality weekly report.

[16]  M. Pallen,et al.  SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse , 2021, Nature Microbiology.

[17]  A. Oliver,et al.  Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 , 2021, Nature.

[18]  A. Sheikh,et al.  SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness , 2021, The Lancet.

[19]  M. V. Van Kerkhove,et al.  Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021 , 2021, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[20]  S. Mallapaty.  India’s neighbours race to sequence genomes as COVID surges , 2021, Nature.

[21]  A. Rebai,et al.  A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa , 2021, medRxiv.

[22]  A. Maxmen.  Why some researchers oppose unrestricted sharing of coronavirus genome data , 2021, Nature.

[23]  L. Abu-Raddad,et al.  Effectiveness of the BNT162b2 Covid-19 Vaccine against the B.1.1.7 and B.1.351 Variants , 2021, The New England journal of medicine.

[24]  Nuno R. Faria,et al.  Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2 , 2021, PLoS biology.

[25]  Samir N. Patel,et al.  S-Gene Target Failure as a Marker of Variant B.1.1.7 Among SARS-CoV-2 Isolates in the Greater Toronto Area, December 2020 to March 2021. , 2021, JAMA.

[26]  B. Ebenso,et al.  Africa needs more genome sequencing to tackle new variants of SARS-CoV-2 , 2021, Nature Medicine.

[27]  Graham W. Taylor,et al.  Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England , 2021, Nature.

[28]  R. Lanfear,et al.  Want to track pandemic variants faster? Fix the bioinformatics bottleneck , 2021, Nature.

[29]  M. Biggerstaff,et al.  Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021 , 2021, MMWR. Morbidity and mortality weekly report.

[30]  P. Febbo,et al.  Genomic surveillance at scale is required to detect newly emerging strains at an early timepoint , 2021 .

[31]  W. Guan,et al.  Effectiveness of inactivated SARS-CoV-2 vaccines against the Delta variant infection in Guangzhou: a test-negative case–control real-world study , 2021, Emerging microbes & infections.

[32]  Carl A. B. Pearson,et al.  Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England , 2021, Science.

[33]  Nina Schwalbe,et al.  Data Sharing and Global Public Health: Defining What We Mean by Data , 2020, Frontiers in Digital Health.

[34]  Evelien M. Adriaenssens,et al.  Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management , 2020, medRxiv.

[35]  Yiming Bao,et al.  The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR , 2020, bioRxiv.

[36]  Edward C. Holmes,et al.  A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology , 2020, Nature Microbiology.

[37]  Trevor Bedford,et al.  Ten recommendations for supporting open pathogen genomic analysis in public health , 2020, Nature Medicine.

[38]  E. Holmes,et al.  A new coronavirus associated with human respiratory disease in China , 2020, Nature.

[39]  V. Stein,et al.  iFLinkC: an iterative functional linker cloning strategy for the combinatorial assembly and recombination of linker peptides with functional domains , 2020, Nucleic acids research.

[40]  Chris Armit,et al.  Increased interactivity and improvements to the GigaScience database, GigaDB , 2018, bioRxiv.

[41]  Wei Li,et al.  gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data , 2018, Nucleic Acids Res..

[42]  Barton E Slatko,et al.  Overview of Next‐Generation Sequencing Technologies , 2018, Current protocols in molecular biology.

[43]  Trevor Bedford,et al.  Nextstrain: real-time tracking of pathogen evolution , 2017, bioRxiv.

[44]  Stefan Elbe,et al.  Data, disease and diplomacy: GISAID's innovative contribution to global health , 2017, Global challenges.

[45]  Alejandro A. Schäffer,et al.  Virus Variation Resource – improved response to emergent viral outbreaks , 2016, Nucleic Acids Res..

[46]  M. Yahia.  Saudi Arabia , 2016, Nature.

[47]  Guidance for representative and targeted genomic SARS-CoV-2 monitoring , 2021 .

[48]  Genomic sequencing of SARS-CoV-2 , 2021 .

[49]  R. Evans.  European Centre for Disease Prevention and Control. , 2014, Nursing standard (Royal College of Nursing (Great Britain) : 1987).