Virological

Topic	Replies	Views	Activity
Issues with SARS-CoV-2 sequencing data nCoV-2019 Genomic Epidemiology	15	72018	April 5, 2022
nCoV's relationship to bat coronaviruses & recombination signals (no snakes) - no evidence the 2019-nCoV lineage is recombinant nCoV-2019 Evolutionary History	23	92716	February 25, 2020
Novel 2019 coronavirus genome SARS-CoV-2 coronavirus	27	424336	February 5, 2020
Response to “On the origin and continuing evolution of SARS-CoV-2” nCoV-2019 Genomic Epidemiology	11	125922	March 16, 2020
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 [email protected] This is a brief report outlining a simple phylogenetic analysis of publicly shared genome…	17	151824	April 2, 2020
nCoV-2019 Spike Protein Receptor Binding Domain Shares High Amino Acid Identity With a Coronavirus Recovered from a Pangolin Viral Metagenomic Dataset nCoV-2019 Evolutionary History	22	61264	February 27, 2020
Identification of a common deletion in the spike protein of SARS-CoV-2 SARS-CoV-2 Molecular Evolution	15	16541	June 24, 2020
Mutations arising in SARS-CoV-2 spike on sustained human-to-human transmission and human-to-animal passage SARS-CoV-2 coronavirus	12	65427	February 22, 2022
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 nCoV-2019 Diagnostics and Vaccines	52	32190	June 21, 2021
Masking strategies for SARS-CoV-2 alignments Software and Tools	17	21661	September 28, 2021
Gained stops in data from The Peter Doherty Institute for Infection and Immunity Genome Reports	11	7472	January 26, 2021
DRC-2018-Viral Genome Characterization Ebolavirus	12	15349	May 23, 2019
Ebola virus disease case in Equateur Province, DRC is a new spillover Ebolavirus	9	16766	February 5, 2024
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 SARS-CoV-2 coronavirus	10	26482	March 16, 2021
Phylogeography of 2014-2015 Ebola virus epidemic Ebolavirus Epidemic 2014-2016	21	14701	February 26, 2016
Missing G21987A mutation in SARS-CoV-2 delta variants due to non-specific amplification by ARTIC v3 primers nCoV-2019 Genomic Epidemiology	11	10931	October 20, 2021
Strong dependence between ZIKV molecular rate estimates and host source of viral sequences Zika virus	24	9861	March 14, 2016
Updated phylogeography Zika virus	28	9063	November 16, 2017
Zika Virus isolate nomenclature and annotation Zika virus	21	9119	March 12, 2016
Illumina whole-genome sequence of Monkeypox virus in a patient travelling from the Canary Islands to France Genome Reports	9	11696	June 13, 2022
WHO Statement on Data Sharing Ebolavirus	19	8084	May 18, 2016
Initial Zika Phylogeography Zika virus	13	8633	August 26, 2016
Early release - 21 new EBOV genomes from Sierra Leone Ebolavirus Epidemic 2014-2016	14	6370	December 18, 2014
Pre-release - Thirteen EBOV genomes from Nigeria 2014 Ebolavirus Epidemic 2014-2016	16	5509	October 19, 2015
Important NYT article Ebolavirus Epidemic 2014-2016	9	6753	February 3, 2015
Ebola virus/H.sapiens-wt/LBR/2014/Makona-201403007 Ebolavirus Epidemic 2014-2016	11	5215	December 5, 2014
ZIKV sequence from Florida Zika virus	10	5388	October 5, 2016
On the veracity of RaTG13 nCoV-2019 Evolutionary History	8	17819	September 19, 2020
Recombinant SARS-CoV-2 genomes involving lineage B.1.1.7 in the UK SARS-CoV-2 Molecular Evolution	0	28648	March 17, 2021
Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings nCoV-2019 Genomic Epidemiology	1	188224	January 25, 2021
August 2022 EVD case in DRC linked to 2018-2020 Nord Kivu EVD outbreak Ebolavirus	0	10818	August 22, 2022
Exploring the natural origins of SARS-CoV-2 nCoV-2019 Evolutionary History	0	13036	January 16, 2021
Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations nCoV-2019 Genomic Epidemiology	4	421475	December 21, 2020
First monkeypox virus genome sequence from Brazil Genome Reports	0	14050	June 9, 2022
Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus MPXV	2	77038	June 22, 2022
Genomic epidemiology of hCoV-19 in Guangdong Province, China nCoV-2019 Genomic Epidemiology	0	12737	March 9, 2020
Outbreak.info: SARS-CoV-2 Mutation Situation Reports Software	2	11247	April 5, 2021
Divergence of nCoV-2019 to closest non-human relative nCoV-2019 Evolutionary History	2	15713	February 12, 2020
First cases of coronavirus disease (COVID-19) in Brazil, South America (2 genomes, 3rd March 2020) Genome Reports	1	96247	February 29, 2020
The Proximal Origin of SARS-CoV-2 nCoV-2019 Evolutionary History	4	249944	March 18, 2020
Multi-country outbreak of Monkeypox virus: genetic divergence and first signs of microevolution Genome Reports	7	50129	May 30, 2022
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) nCoV-2019 Genomic Epidemiology	2	33873	April 25, 2021
Initial observations about putative APOBEC3 deaminase editing driving short-term evolution of MPXV since 2017 Evolution	6	39158	May 31, 2022
Introducing Pathoplexus Software	0	3101	August 27, 2024
Preliminary analysis of SARS-CoV-2 importation & establishment of UK transmission lineages nCoV-2019 Genomic Epidemiology	6	61957	June 26, 2020
Early appearance of two distinct genomic lineages of SARS-CoV-2 in different Wuhan wildlife markets suggests SARS-CoV-2 has a natural origin SARS-CoV-2 coronavirus	3	45188	June 7, 2021
An APOBEC3 molecular clock to estimate the date of emergence of hMPXV Evolution	0	13739	August 6, 2022
First draft genome sequence of Monkeypox virus associated with the suspected multi-country outbreak, May 2022 (confirmed case in Portugal) Genome Reports	0	76941	May 19, 2022
Response to nCoV2019 Against Backdrop of Endogenous Retroviruses nCoV-2019 Evolutionary History	1	53599	February 14, 2020
Selection analysis identifies significant mutational changes in Omicron that are likely to influence both antibody neutralization and Spike function (Part 1 of 2) SARS-CoV-2 coronavirus	1	25974	January 20, 2022

Issues with SARS-CoV-2 sequencing data

nCoV-2019 Genomic Epidemiology

15

72018

April 5, 2022

nCoV's relationship to bat coronaviruses & recombination signals (no snakes) - no evidence the 2019-nCoV lineage is recombinant

nCoV-2019 Evolutionary History

23

92716

February 25, 2020

Novel 2019 coronavirus genome

SARS-CoV-2 coronavirus

27

424336

February 5, 2020

Response to “On the origin and continuing evolution of SARS-CoV-2”

nCoV-2019 Genomic Epidemiology

11

125922

March 16, 2020

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 [email protected] This is a brief report outlining a simple phylogenetic analysis of publicly shared genome…