Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States.
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3,302 citations
Cites background from "Coast-to-Coast Spread of SARS-CoV-2..."
..., 2013), and SARS-CoV-2 sequence diversity is very low (Fauver et al., 2020)....
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1,517 citations
Cites background from "Coast-to-Coast Spread of SARS-CoV-2..."
...These genomic sequences have been useful for understanding viral emergence and spread (Andersen et al., 2020; Bedford et al., 2020; Fauver et al., 2020), but the lack of corresponding high-throughput...
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1,285 citations
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References
272,030 citations
16,857 citations
"Coast-to-Coast Spread of SARS-CoV-2..." refers background in this paper
...A novel coronavirus, known as SARS-CoV-2, was identified as the cause of an outbreak of pneumonia in Wuhan, China, in December 2019 (Gorbalenya et al., 2020; Wu et al., 2020; Zhou et al., 2020)....
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13,668 citations
"Coast-to-Coast Spread of SARS-CoV-2..." refers methods in this paper
...Specifically, we aligned sequences using mafft (Katoh et al., 2002), masked sites at the 50 and 30 ends of the alignment as well as a small number of sites that likely vary due to assembly artifacts (see https://github.com/nextstrain/ncov), and reconstructed a phylogeny using IQ-Tree (Nguyen et al., 2015)....
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...…NCBI https://www.ncbi.nlm.nih.gov/bioproject/ PRJNA614976 Software and Algorithms R CRAN https://cran.r-project.org/ IQ-Tree http://www.iqtree.org/ Nguyen et al., 2015 augur toolkit https://bedford.io/projects/augur/ Hadfield et al., 2018 MAFFT https://mafft.cbrc.jp/alignment/software/ Katoh et…...
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...4.1 Flow cell Oxford Nanopore Tech FLO-MIN106D Blunt/TA Ligase Master Mix New England BioLabs MO367L NEBNext Ultra II End Repair/dA-Tailing Module New England BioLabs E7546S NEBNext Quick Ligation Module New England BioLabs E6056S Deposited Data International COVID-19 cases ECDC https://ourworldindata.org/ coronavirus-source-data U.S. COVID-19 cases JHU Dong et al., 2020 Air passenger volumes (commercial) IATA https://www.iata.org/pages/default.aspx SARS-CoV-2 Genomes GISAID (EPI_ISL_416416-416424) https://www.gisaid.org/ SARS-CoV-2 Sequencing Data SRA, NCBI https://www.ncbi.nlm.nih.gov/bioproject/ PRJNA614976 Software and Algorithms R CRAN https://cran.r-project.org/ IQ-Tree http://www.iqtree.org/ Nguyen et al., 2015 augur toolkit https://bedford.io/projects/augur/ Hadfield et al., 2018 MAFFT https://mafft.cbrc.jp/alignment/software/ Katoh et al., 2002 treetime https://github.com/neherlab/treetime Sagulenko et al., 2018 RAMPART ARTIC Network https://github.com/artic-network/rampart ARTIC Network Bioinformatic protocol ARTIC Network https://artic.network/ncov-2019/ ncov2019-bioinformatics-sop.html Nextstrain https://nextstrain.org/ Hadfield et al., 2018 Other Amplicon sequencing protocol PrimalSeq Quick et al., 2017...
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...…we aligned sequences using mafft (Katoh et al., 2002), masked sites at the 50 and 30 ends of the alignment as well as a small number of sites that likely vary due to assembly artifacts (see https://github.com/nextstrain/ncov), and reconstructed a phylogeny using IQ-Tree (Nguyen et al., 2015)....
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12,003 citations
"Coast-to-Coast Spread of SARS-CoV-2..." refers background or methods in this paper
...Specifically, we aligned sequences using mafft (Katoh et al., 2002), masked sites at the 50 and 30 ends of the alignment as well as a small number of sites that likely vary due to assembly artifacts (see https://github.com/nextstrain/ncov), and reconstructed a phylogeny using IQ-Tree (Nguyen et…...
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...…Nguyen et al., 2015 augur toolkit https://bedford.io/projects/augur/ Hadfield et al., 2018 MAFFT https://mafft.cbrc.jp/alignment/software/ Katoh et al., 2002 treetime https://github.com/neherlab/treetime Sagulenko et al., 2018 RAMPART ARTIC Network…...
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9,231 citations
"Coast-to-Coast Spread of SARS-CoV-2..." refers background in this paper
...A novel coronavirus, known as SARS-CoV-2, was identified as the cause of an outbreak of pneumonia in Wuhan, China, in December 2019 (Gorbalenya et al., 2020; Wu et al., 2020; Zhou 990 Cell 181, 990–996, May 28, 2020 ª 2020 Elsevier Inc. et al., 2020)....
[...]
...A novel coronavirus, known as SARS-CoV-2, was identified as the cause of an outbreak of pneumonia in Wuhan, China, in December 2019 (Gorbalenya et al., 2020; Wu et al., 2020; Zhou et al., 2020)....
[...]