nCoV-2019 Genomic Epidemiology

Topic	Replies	Views	Activity
Phylodynamic Analysis \| 176 genomes \| 6 Mar 2020 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…	17	116770	April 2, 2020
About the nCoV-2019 Genomic Epidemiology category	0	2157	January 31, 2020
SARS-CoV-2 lineage assignment is more stable with UShER	0	730	January 20, 2022
Report on Omicron Spike mutations on epitopes and immunological/epidemiological/kinetics effects from literature	0	14182	November 30, 2021
Monitoring the evolution and spread of Delta sublineages AY.25 and AY.27 in Canada	1	2093	November 18, 2021
Issues with SARS-CoV-2 sequencing data	14	42634	November 10, 2021
The SARS-CoV-2 variant Delta displaced the variants Gamma and Gamma plus in Amazonas, Brazil	0	2628	October 26, 2021
Missing G21987A mutation in SARS-CoV-2 delta variants due to non-specific amplification by ARTIC v3 primers	11	4244	October 20, 2021
Evidence Against the Veracity of SARS-CoV-2 Genomes Intermediate between Lineages A and B	0	15593	September 3, 2021
Genomic Surveillance of SARS-CoV-2 in the State of Rio de Janeiro, Brazil: technical briefing	7	7130	September 3, 2021
Emergence of Y453F and Δ69-70HV mutations in a lymphoma patient with long-term COVID-19	4	23187	August 7, 2021
Genomic surveillance tracks the first communitary outbreak of Delta (B.1.617.2) variant in Brazil	1	4052	August 4, 2021
Emergence of a putative novel SARS-CoV-2 P.X lineage harboring N234P and E471Q spike protein mutations in Southern Brazil	0	1545	July 14, 2021
Viral infection and transmission in a large well-traced outbreak caused by the Delta SARS-CoV-2 variant	0	259951	July 7, 2021
Emergence and spread of SARS-CoV-2 P.1 (Gamma) lineage variants carrying Spike mutations 𝚫141-144, N679K or P681H during persistent viral circulation in Amazonas, Brazil	0	6203	July 4, 2021
Detection of Spike Mutations; D80G, T95I, G142D, △144, N439K, E484K, P681H, I1130V, and D1139H, in B.1.1.482 Lineage (AV.1) Samples from South Yorkshire, UK	1	7486	May 23, 2021
Spread of endemic SARS-CoV-2 lineages in Russia	2	5197	May 24, 2021
Identification of SARS-CoV-2 P.1-related lineages in Brazil provides new insights about the mechanisms of emergence of Variants of Concern	0	7327	May 16, 2021
Emergence of SARS-CoV-2 lineage A.27 in Germany, expressing viral spike proteins with several amino acid replacements of interest, including L18F, L452R, and N501Y in the absence of D614G	0	2568	May 14, 2021
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	3	10089	April 28, 2021
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)	2	26233	April 25, 2021
SARS-CoV-2 reinfection by the new Variant of Concern (VOC) P.1 in Amazonas, Brazil	3	47556	January 19, 2021
Detection of the recurrent substitution Q677H in the spike protein of SARS-CoV-2 in cases descended from the lineage B.1.429	0	4291	March 20, 2021
Potential novel SARS-CoV-2 variant of interest from lineage AP.1 with N501Y and additional spike mutations identified in Saxony, Germany	0	3837	April 6, 2021
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	0	6776	April 6, 2021
Detection of a large cluster and multiple introductions of the P.1 SARS-CoV-2 Variant of Concern in Massachusetts	0	6453	April 2, 2021
Detection of the B.1.1.7 and B.1.351 SARS-CoV-2 variants in Bangladesh	0	2964	March 26, 2021
A potential SARS-CoV-2 variant of interest (VOI) harboring mutation E484K in the Spike protein was identified within lineage B.1.1.33 circulating in Brazil	0	10996	March 11, 2021
Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein	2	32236	February 27, 2021
B.1.258∆, a SARS-CoV-2 variant with ∆H69/∆V70 in the Spike protein circulating in the Czech Republic and Slovakia	1	22530	February 11, 2021

Phylodynamic Analysis | 176 genomes | 6 Mar 2020

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…