The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
Temporal signal and the phylodynamic threshold of SARS-CoV-2
Open accessPublished version of a preprint
Abstract
The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publicly available in near real time. Early analyses of these data revealed low sequence variation, a finding that is consistent with a recently emerging outbreak, but which raises the question of whether such data are sufficiently informative for phylogenetic inferences of evolutionary rates and time scales. The phylodynamic threshold is a key concept that refers to the point in time at which sufficient molecular evolutionary change has accumulated in available genome samples to obtain robust phylodynamic estimates. For example, before the phylodynamic threshold is reached, genomic variation is so low that even large amounts of genome sequences may be insufficient to estimate the virus’s evolutionary rate and the time scale of an outbreak. We collected genome sequences of SARS-CoV-2 from public databases at eight different points in time and conducted a range of tests of temporal signal to determine if and when the phylodynamic threshold was reached, and the range of inferences that could be reliably drawn from these data. Our results indicate that by 2 February 2020, estimates of evolutionary rates and time scales had become possible. Analyses of subsequent data sets, that included between 47 and 122 genomes, converged at an evolutionary rate of about 1.1 × 10−3 subs/site/year and a time of origin of around late November 2019. Our study provides guidelines to assess the phylodynamic threshold and demonstrates that establishing this threshold constitutes a fundamental step for understanding the power and limitations of early data in outbreak genome surveillance.
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Self-citationThe proximal origin of SARS-CoV-2
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SARS-CoV-2 variants, spike mutations and immune escape
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Self-citationMarkov, P. V., Ghafari, M., Beer, M., Lythgoe, K., Simmonds, P., Stilianakis, N. I., & Katzourakis, A. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00878-2 · Cited by 1,179
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Self-citationAssignment of epidemiological lineages in an emerging pandemic using the pangolin tool
O’Toole, Á., Scher, E., Underwood, A., Jackson, B., Hill, V., McCrone, J. T., Colquhoun, R., Ruis, C., Abu-Dahab, K., Taylor, B., et al. (2021) · Virus Evolution · doi:10.1093/ve/veab064 · Cited by 1,077
Self-citationEvolution and epidemic spread of SARS-CoV-2 in Brazil
Candido, D. S., Claro, I. M., de Jesus, J. G., Souza, W. M., Moreira, F. R. R., Dellicour, S., Mellan, T. A., du Plessis, L., Pereira, R. H. M., Sales, F. C. S., et al. (2020) · Science · doi:10.1126/science.abd2161 · Cited by 573
“We estimate the date of the common ancestor (TMRCA) of the SARS-CoV-2 pandemic to around mid-November 2019 (median = 19 November 2019, 95% BCI: 26 October 2019 to 6 December 2019), which is consistent with recent findings (34, 35).”
ResultSelf-citation
Metadata
- Authors
- Duchene, S., Featherstone, L., Haritopoulou-Sinanidou, M., Rambaut, A., Lemey, P., & Baele, G.
- Venue
- Virus Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-07-01
- Volume
- 6
- Issue
- 2
- Pages
- veaa061-veaa061
- ISSN
- 2057-1577 (ISSN-L)
- OpenAlex
- W3065795114
- Cited by
- 384
- References
- 32
- FWCI
- 8.90
- Type
- journal article
- Language
- en
- Open access
- gold
- Funders
- Australian Research Council Discovery Early Career Researcher (DE190100805)
- Australian National Health and Medical Research Council (APP1157586)
- Wellcome Trust (206298/Z/17/Z―ARTIC, 725422-ReservoirDOCS, G066215N, G0D5117N, G0B9317N, C14/18/094, G0E1420N)
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- Duchene, S., Featherstone, L., Haritopoulou-Sinanidou, M., Rambaut, A., Lemey, P., & Baele, G. (2020). Temporal signal and the phylodynamic threshold of SARS-CoV-2. Virus Evolution. https://doi.org/10.1093/ve/veaa061
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