Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.
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"Evaluating the Effects of SARS-CoV-..." refers methods in this paper
...Rooted and dated phylogenies were estimated by randomly resolving polytomies in the ML trees described above using ape 5.3(Paradis et al., 2004) and treedater 0.5.1(Volz and Frost, 2017)....
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9,231 citations
"Evaluating the Effects of SARS-CoV-..." refers background in this paper
...This shows the early stages of emergence of D614G into Europe from China....
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...Retrospectively sampled viruses suggest this mutation was present in Guangzhou, Sichuan, and Shanghai Provinces, China in late January (Figure S1)....
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...We included the first sequenced genome of SARS-CoV-2 from China (Wu et al., 2020) as an outgroup to root the tree....
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...It is therefore likely that the D614G mutation occurred in China before being introduced on multiple occasions to European countries (Lai et al., 2020) where it increased in frequency....
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8,124 citations
"Evaluating the Effects of SARS-CoV-..." refers methods in this paper
...Nucleotide evolution was modeled as a strict clock HKY process (Hasegawa et al., 1985)....
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...The HKY model was used to model nucleotide evolution(Hasegawa et al., 1985), and, following Duchene et al....
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5,840 citations
"Evaluating the Effects of SARS-CoV-..." refers background in this paper
...Combined with epidemiological observations of disparities in viral loads in the upper respiratory tract (Lorenzo-Redondo et al., 2020; Wölfel et al., 2020), these results are suggestive of a transmission-mediated fitness differential between spike 614 variants....
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5,492 citations
"Evaluating the Effects of SARS-CoV-..." refers methods in this paper
...Convergence was assessed using Tracer(Rambaut et al., 2018) prior to further analysis....
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...10.5 (Suchard et al., 2018) https://beast.community/ Tracer (Rambaut et al., 2018) https://beast.community/ BEAST2 PhyDyn (Bouckaert et al., 2019; Volz and Siveroni, 2018) https://github.com/mrc-ide/PhyDyn ARTIC network protocol ARTIC network https://artic.network/ncov-2019 R packages (treedater 0.5.1, ape package v. 5.3, brms v. 2.13.5, rstan v. 2.21.2, SPIn v. 1.1, skygrowth 0.3.1) (Paradis and Schliep, 2019; Volz and Frost, 2017; Bürkner, 2018; Stan Development Team, 2020; Liu et al., 2015; Volz and Didelot, 2018) http://www.R-project.org; https://github.com/mrc-ide/skygrowth IQtree 1.6.12 (Minh et al., 2020; Rambaut et al., 2020) http://www.iqtree.org/ MRC-CLIMB (Connor et al., 2016) https://www.climb.ac.uk/ Nextflow pipeline for processing/ assembly of ARTIC protocol amplicons https://github.com/connor-lab/ncov2019artic-nf https://github.com/connor-lab/ ncov2019-artic-nf...
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