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Using multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data.
Inward, Rhys P D; Parag, Kris V; Faria, Nuno R.
  • Inward RPD; Department of Zoology, University of Oxford, Oxford, UK. rhys.inward@zoo.ox.ac.uk.
  • Parag KV; MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK. k.parag@imperial.ac.uk.
  • Faria NR; NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK. k.parag@imperial.ac.uk.
Nat Commun ; 13(1): 5587, 2022 09 23.
Article in English | MEDLINE | ID: covidwho-2042320
ABSTRACT
The choice of viral sequences used in genetic and epidemiological analysis is important as it can induce biases that detract from the value of these rich datasets. This raises questions about how a set of sequences should be chosen for analysis. We provide insights on these largely understudied problems using SARS-CoV-2 genomic sequences from Hong Kong, China, and the Amazonas State, Brazil. We consider multiple sampling schemes which were used to estimate Rt and rt as well as related R0 and date of origin parameters. We find that both Rt and rt are sensitive to changes in sampling whilst R0 and the date of origin are relatively robust. Moreover, we find that analysis using unsampled datasets result in the most biased Rt and rt estimates for both our Hong Kong and Amazonas case studies. We highlight that sampling strategy choices may be an influential yet neglected component of sequencing analysis pipelines.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study Limits: Humans Country/Region as subject: South America / Asia / Brazil Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2022 Document Type: Article Affiliation country: S41467-022-32812-0

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study Limits: Humans Country/Region as subject: South America / Asia / Brazil Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2022 Document Type: Article Affiliation country: S41467-022-32812-0