arXiv 1 Oct 2021 · Econometrics · publishedEconometrics Journal (2022) · 23 citations (OpenAlex)
arXiv:2110.00533 · PDF · DOI · OpenAlex · Extracted main text
We propose a simple dynamic model for estimating the relative contagiousness of two virus variants. Maximum likelihood estimation and inference is conveniently invariant to variation in the total number of cases over the sample period and can be expressed as a logistic regression. We apply the model to Danish SARS-CoV-2 variant data. We estimate the reproduction numbers of Alpha and Delta to be larger than that of the ancestral variant by a factor of 1.51 [CI 95%: 1.50, 1.53] and 3.28 [CI 95%: 3.01, 3.58], respectively. In a predominately vaccinated population, we estimate Omicron to be 3.15 [CI 95%: 2.83, 3.50] times more infectious than Delta. Forecasting the proportion of an emerging virus variant is straight forward and we proceed to show how the effective reproduction number for a new variant can be estimated without contemporary sequencing results. This is useful for assessing the state of the pandemic in real time as we illustrate empirically with the inferred effective reproduction number for the Alpha variant.
appendix boundary found by appendix_command · 82% of the source is main text. Read the extracted text to check this.
The works this paper leans on most, across its whole bibliography — not restricted to papers in our corpus. Ranked by composite intensity, which combines how often a work is mentioned, how many sections mention it, and how much of that falls in the main text rather than the appendix.
| Reference | Intensity | Mentions | Sections | Main text | |
|---|---|---|---|---|---|
| 1 | E. Volz, S. Mishra, M. Chand, J. C. Barrett, R. Johnson, L. Geidelbe… (2021) Transmission of SARS-CoV-2 lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data | 0.737 | 3 | 2 | 100% |
| 2 | M. Besancon, D. Anthoff, A. Arslan, S. Byrne, D. Lin, T. Papamarkou,… (2019) Distributions.jl: Definition and modeling of probability distributions in the JuliaStats ecosystem | 0.405 | 1 | 1 | 100% |
| 3 | A. Rambaut, N. Loman, O. Pybus, W. Barclay, J. Barrett, A. Carabelli… (2020) Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations | 0.405 | 1 | 1 | 100% |
| 4 | P. Bager, J. Wohlfahrt, J. Fonager, M. Albertsen, T. Yssing Michaels… (2021) Increased risk of hospitalisation associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark | 0.405 | 1 | 1 | 100% |
| 5 | P. R. Hansen (2022) Replication files for `relative contagiousness of emerging virus variants: An analysis of the Alpha, Delta, and Omicron SARS-CoV… self | 0.405 | 1 | 1 | 100% |
| 6 | F. P. Lyngse, K. Mlbak, M. Denwood, L. E. Christiansen, C. H. Mller,… (2022) Effect of vaccination on household transmission of SARS-CoV-2 Delta VOC | 0.405 | 1 | 1 | 100% |
| 7 | H. Nishiura, K. Ito, A. Anzai, T. Kobayashi, C. Piantham, A. J. Rodr… (2022) Relative reproduction number of SARS-CoV-2 Omicron (B.1.1.529) compared with Delta variant in South Africa | 0.405 | 1 | 1 | 100% |
| 8 | R. Viana, S. Moyo, D. G. Amoako, H. Tegally, C. Scheepers, C. L. Alt… (2022) Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa | 0.405 | 1 | 1 | 100% |
| 9 | R Core Team, R: A Language and Environment for Statistical Computing… (2018) R: A Language and Environment for Statistical Computing | 0.405 | 1 | 1 | 100% |
| 10 | Statens Serum Institut, Ekspertrapport af d. 23. oktober (2020) Ekspertrapport af d. 23. oktober 2020: Incidens og fremskrivning af COVID-19 tilflde | 0.405 | 1 | 1 | 100% |
Showing the top 10 of 15 scored citations.