Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia
Top Cited Papers
Open Access
- 28 January 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Communications
- Vol. 12 (1), 1-13
- https://doi.org/10.1038/s41467-020-20880-z
Abstract
The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use of phylogenetics to understand and control its spread. Here, we analyze the emergence of SARS-CoV-2 in Russia in March and April 2020. Combining phylogeographic analysis with travel history data, we estimate that the sampled viral diversity has originated from at least 67 closely timed introductions into Russia, mostly in late February to early March. All but one of these introductions were not from China, suggesting that border closure with China has helped delay establishment of SARS-CoV-2 in Russia. These introductions resulted in at least 9 distinct Russian lineages corresponding to domestic transmission. A notable transmission cluster corresponded to a nosocomial outbreak at the Vreden hospital in Saint Petersburg; phylodynamic analysis of this cluster reveals multiple (2-3) introductions each giving rise to a large number of cases, with a high initial effective reproduction number of 3.0 [1.9, 4.3].Funding Information
- Russian Foundation for Basic Research (20-04-60556)
This publication has 31 references indexed in Scilit:
- Reconstruction and prediction of viral disease epidemicsEpidemiology and Infection, 2018
- Minimap2: pairwise alignment for nucleotide sequencesBioinformatics, 2018
- TreeTime: Maximum-likelihood phylodynamic analysisVirus Evolution, 2018
- Genomic epidemiology reveals multiple introductions of Zika virus into the United StatesNature, 2017
- ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic DataMolecular Biology and Evolution, 2016
- IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood PhylogeniesMolecular Biology and Evolution, 2014
- A New Framework and Software to Estimate Time-Varying Reproduction Numbers During EpidemicsAmerican Journal of Epidemiology, 2013
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and UsabilityMolecular Biology and Evolution, 2013
- Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)Proceedings of the National Academy of Sciences of the United States of America, 2012
- A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing dataBioinformatics, 2011