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Phylodynamic Analysis | 176 genomes | 6 Mar 2020
nCoV-2019 Genomic Epidemiology

Phylogenetic analysis of nCoV-2019 genomes 6-Mar-2020 Andrew Rambaut, University of Edinburgh, Edinburgh UK a.rambaut@ed.ac.uk This is a brief report outlining a simple phylogenetic analysis of publicly shared genome…

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Stepwise evolution and exceptional conservation of ORF1a/b overlap
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Early appearance of two distinct genomic lineages of SARS-CoV-2 in different Wuhan wildlife markets suggests SARS-CoV-2 has a natural origin
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Preliminary in silico assessment of the specificity of published molecular assays and design of new assays using the available whole genome sequences of 2019-nCoV
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Genomic Surveillance of SARS-CoV-2 in the State of Rio de Janeiro, Brazil: technical briefing
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Spread of endemic SARS-CoV-2 lineages in Russia
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The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the Spike protein
nCoV-2019 Genomic Epidemiology
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Mutations arising in SARS-CoV-2 spike on sustained human-to-human transmission and human-to-animal passage
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Novel sublineage within B.1.1.1 currently expanding in Peru and Chile, with a convergent deletion in the ORF1a gene (Δ3675-3677) and a novel deletion in the Spike gene (Δ246-252, G75V, T76I, L452Q, F490S, T859N)
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SARS-CoV-2 reinfection by the new Variant of Concern (VOC) P.1 in Amazonas, Brazil
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Outbreak.info: SARS-CoV-2 Mutation Situation Reports
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Release - 4 EBOV genomes from Guinea 2021 outbreak
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Phylogenetic and Recombination Analysis of SARS-CoV-2-like Viruses
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Masking strategies for SARS-CoV-2 alignments
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Issues with SARS-CoV-2 sequencing data
nCoV-2019 Genomic Epidemiology
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Detection of the recurrent substitution Q677H in the spike protein of SARS-CoV-2 in cases descended from the lineage B.1.429
nCoV-2019 Genomic Epidemiology
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CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes
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Potential novel SARS-CoV-2 variant of interest from lineage AP.1 with N501Y and additional spike mutations identified in Saxony, Germany
nCoV-2019 Genomic Epidemiology
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Increasing frequency of SARS-CoV-2 lineages B.1.1.7, P.1 and P.2 and identification of a novel lineage harboring E484Q and N501T spike mutations in Minas Gerais, Southeast Brazil
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Identification of a new B.1.1.33 SARS-CoV-2 Variant of Interest (VOI) circulating in Brazil with mutation E484K and multiple deletions in the amino (N)-terminal domain of the Spike protein
nCoV-2019 Genomic Epidemiology
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Ready-to-use global platform for variant detection in SARS-CoV-2
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Global framework for SARS-CoV-2 data analysis: Application to intrahost variation | Part 2
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Detection of a large cluster and multiple introductions of the P.1 SARS-CoV-2 Variant of Concern in Massachusetts
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Genomic characterisation of sylvatic yellow fever virus epizootic in Trinidad
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Detection of the B.1.1.7 and B.1.351 SARS-CoV-2 variants in Bangladesh
nCoV-2019 Genomic Epidemiology
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Assemblies of putative SARS-CoV2-spike-encoding mRNA sequences for vaccines BNT-162b2 and mRNA-1273
nCoV-2019 Diagnostics and Vaccines
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Recombinant SARS-CoV-2 genomes involving lineage B.1.1.7 in the UK
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Pango Lineage Nomenclature: provisional rules for naming recombinant lineages
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Integration of JBrowse 2 genome browser with Nextstrain
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Tracking SARS-CoV-2 VOC 202012/01 (lineage B.1.1.7) dissemination in Portugal: insights from nationwide RT-PCR Spike gene drop out data
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