An integrated national scale SARS-CoV-2 genomic surveillance network

Robson, Samuel; Scarlett, Garry; Bourgeois, Yann; Beckett, Angela H.

doi:10.1016/s2666-5247(20)30054-9

Cited by 255 publications

(150 citation statements)

References 7 publications

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“…Sample collection and sequencing. We utilized data from the Coronavirus Disease 2019 (COVID-19) Genomics UK Consortium (CoG-UK) [16] , a partnership of more than 18 academic, medical and public health research centres contributing sequencing and analysis capabilities. Sequence data was generated from a variety of protocols and platforms and were uploaded to a centralized environment for storage and analysis (MRC-CLIMB) ( https://www.climb.ac.uk/ ) [24] .…”

Section: Methodsmentioning

confidence: 99%

“…In the UK, the early creation of a national sequencing collaboration, CoG-UK [16] , has seen the production of over 30,000 SARS-CoV-2 sequences from across the country in less than 5 months. CoG-UK has enabled the usage of consistent sampling, shared bioinformatic and laboratory approaches, and the collection of the same core set of metadata for all samples.…”

Section: Introductionmentioning

confidence: 99%

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Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity

Volz

Hill

McCrone

et al. 2020

Preprint

281

312

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In February 2020 a substitution at the interface between SARS-CoV-2 Spike protein subunits, Spike D614G, was observed in public databases. The Spike 614G variant subsequently increased in frequency in many locations throughout the world. Global patterns of dispersal of Spike 614G are suggestive of a selective advantage of this variant, however the origin of Spike 614G is associated with early colonization events in Europe and subsequent radiations to the rest of the world. Increasing frequency of 614G may therefore be due to a random founder effect. We investigate the hypothesis for positive selection of Spike 614G at the level of an individual country, the United Kingdom, using more than 25,000 whole genome SARS-CoV-2 sequences collected by COVID-19 Genomics UK Consortium. Using phylogenetic analysis, we identify Spike 614G and 614D clades with unique origins in the UK and from these we extrapolate and compare growth rates of co-circulating transmission clusters. We find that Spike 614G clusters are introduced in the UK later on average than 614D clusters and grow to larger size after adjusting for time of introduction. Phylodynamic analysis does not show a significant increase in growth rates for clusters with the 614G variant, but population genetic modelling indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We also investigate the potential influence of Spike 614D versus G on virulence by matching a subset of records to clinical data on patient outcomes. We do not find any indication that patients infected with the Spike 614G variant have higher COVID-19 mortality, but younger patients have slightly increased odds of 614G carriage. Despite the availability of a very large data set, well represented by both Spike 614 variants, not all approaches showed a conclusive signal of higher transmission rate for 614G, but significant differences in growth, size, and composition of these lineages indicate a need for continued study.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity

Volz

Hill

McCrone

et al. 2020

Preprint

281

312

View full text Add to dashboard Cite

show abstract

“…Either way, by combining different levels of expertise, consolidated laboratories not only processed large volumes of sam ples but also supported surveillance systems 102 . Although the best surveillance system still needs to be defined, the setting up of networks of regional sequencing centres hosted in academic institutions and/or public health agencies provided a close to real time sequencing facility that enabled genomic data to be interpreted and used locally for epidemiological monitoring 103 . The large scale use of such sequencing centres in Europe for the assessment of how the virus interacts with host cofactors and the health consequences of COVID19 are continuously expanded and improved 104 .…”

Section: Implementation Of New Testsmentioning

confidence: 99%

Considerations for diagnostic COVID-19 tests

et al. 2020

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During the early phase of the coronavirus disease 2019 (COVID-19) pandemic, design, development, validation, verification and implementation of diagnostic tests were actively addressed by a large number of diagnostic test manufacturers. Hundreds of molecular tests and immunoassays were rapidly developed, albeit many still await clinical validation and formal approval. In this Review, we summarize the crucial role of diagnostic tests during the first global wave of COVID-19. We explore the technical and implementation problems encountered during this early phase in the pandemic, and try to define future directions for the progressive and better use of (syndromic) diagnostics during a possible resurgence of COVID-19 in future global waves or regional outbreaks. Continuous global improvement in diagnostic test preparedness is essential for more rapid detection of patients, possibly at the point of care, and for optimized prevention and treatment, in both industrialized countries and low-resource settings.

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“…Currently, ViruSurf includes reference sequences from RefSeq ( 5 ) and regular sequences from GenBank ( 6 ) of SARS-CoV-2 and SARS-related coronavirus, as well as MERS-CoV, Ebola and Dengue viruses; the pipeline is generic and other virus species will be progressively added next, giving precedence to those species which are most harmful to humans. For what concerns SARS-CoV-2, we also include sequences from COG-UK ( 7 ) and NMDC ( http://nmdc.cn/ ). GenBank and COG-UK data are made publicly available and can be freely downloaded and re-distributed.…”

Section: Introductionmentioning

confidence: 99%

ViruSurf: an integrated database to investigate viral sequences

Canakoglu

Pinoli

Bernasconi

et al. 2020

Nucleic Acids Research

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ViruSurf, available at http://gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database, available at http://gmql.eu/virusurf_gisaid/, offers a subset of these functionalities. Given the current pandemic outbreak, SARS-CoV-2 data are collected from the four sources; but ViruSurf contains other virus species harmful to humans, including SARS-CoV, MERS-CoV, Ebola and Dengue. The database is centered on sequences, described from their biological, technological and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences. Several example queries on the database confirm and possibly improve results from recent research papers; results can be recomputed over time and upon selected populations. Effective search over large and curated sequence data may enable faster responses to future threats that could arise from new viruses.

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An integrated national scale SARS-CoV-2 genomic surveillance network

Abstract: Trust. The goal of this consortium is to sequence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for up to 230 000 patients, health-care workers, and other essential workers in the UK with COVID-19, which will help to enable the tracking of SARS-CoV-2 transmission,

Cited by 255 publications

References 7 publications

Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity

Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity

Considerations for diagnostic COVID-19 tests

ViruSurf: an integrated database to investigate viral sequences

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