Genomic surveillance at scale is required to detect newly emerging strains at an early timepoint
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Abstract
Genomic surveillance in the setting of the coronavirus disease 2019 (COVID-19) pandemic has the potential to identify emerging SARS-CoV-2 strains that may be more transmissible, virulent, evade detection by standard diagnostic tests, or vaccine escapes. The rapid spread of the SARS-CoV-2 B.1.1.7 strain from southern England to other parts of the country and globe is a clear example of the impact of such strains. Early discovery of the B.1.1.7 strain was enabled through the proactive COVID-19 Genomics UK (COG-UK) program and the UK’s commitment to genomic surveillance, sequencing about 10% of positive samples. 1 In order to enact more aggressive public health measures to minimize the spread of such strains, genomic surveillance needs to be of sufficient scale to detect early emergence and expansion in the broader virus population. By modeling common performance characteristics of available diagnostic and sequencing tests, we developed a model that assesses the sampling required to detect emerging strains when they are less than 1% of all strains in a population. This model demonstrates that 5% sampling of all positive tests allows the detection of emerging strains when they are a prevalence of 0.1% to 1.0%. While each country will determine their risk tolerance for the emergence of novel strains, as vaccines are distributed and we work to end the pandemic and prevent future SARS-CoV-2 outbreaks, genomic surveillance will be an integral part of success.
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SciScore for 10.1101/2021.01.12.21249613: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The primary limitation is vaccine availability, and although vaccine developers are ramping up supply as quickly as possible, it will take time to produce the huge volume of doses needed. Further, safety and efficacy in some populations, such as children, has not yet been established. As vaccines are delivered, there is now a selective …
SciScore for 10.1101/2021.01.12.21249613: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The primary limitation is vaccine availability, and although vaccine developers are ramping up supply as quickly as possible, it will take time to produce the huge volume of doses needed. Further, safety and efficacy in some populations, such as children, has not yet been established. As vaccines are delivered, there is now a selective pressure and risk for vaccine escape variants. Immune escape variants have been recently reported in patients treated for COVID-19 infection.23, 24 Thus, genomic surveillance for vaccine escapes is now critically important as undetected emergence of a vaccine escape strain could hinder the ability to end this pandemic. As vaccination timelines will vary between countries, it will remain important to continue surveillance for these variants even once a country is fully vaccinated as there could be introductions from unvaccinated individuals travelling from countries with lower vaccination rates. Our model is based on many assumptions that may or may not be valid for specific regions and/or countries. We also make assumptions that are idealistic such as minimized sampling bias with similar distributions of any relevant sample, patient, and viral characteristics across populations. As with any model, it is imperfect. It is proposed to help demonstrate the value that sequencing just 5% of positive samples provides to public health officials and other stakeholders in order to set a goal for genomic surveillance. Genomic surveillance, based on sequen...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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