# nCoV-2019 Genomic Epidemiology **URL:** https://virological.org/c/novel-2019-coronavirus/ncov-2019-genomic-epidemiology/36.md?page=1 [Latest](https://virological.org/latest.md) · [Categories](https://virological.org/categories.md) **Page:** 2 --- ## [Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein](https://virological.org/t/phylogenetic-relationship-of-sars-cov-2-sequences-from-amazonas-with-emerging-brazilian-variants-harboring-mutations-e484k-and-n501y-in-the-spike-protein/585)
**Author:** [@paola](https://virological.org/u/paola)\ **Replies:** 2\ **Last updated:** [February 27, 2021, 2:11am UTC](https://virological.org/t/phylogenetic-relationship-of-sars-cov-2-sequences-from-amazonas-with-emerging-brazilian-variants-harboring-mutations-e484k-and-n501y-in-the-spike-protein/585 "2021-02-27T02:11:25Z")
Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein Felipe Naveca 1, Valdinete Nascimento 1, Victor Souza 1, André C… --- ## [B.1.258∆, a SARS-CoV-2 variant with ∆H69/∆V70 in the Spike protein circulating in the Czech Republic and Slovakia](https://virological.org/t/b-1-258-a-sars-cov-2-variant-with-h69-v70-in-the-spike-protein-circulating-in-the-czech-republic-and-slovakia/613)
**Author:** [@tvinar](https://virological.org/u/tvinar)\ **Replies:** 1\ **Last updated:** [February 11, 2021, 9:35pm UTC](https://virological.org/t/b-1-258-a-sars-cov-2-variant-with-h69-v70-in-the-spike-protein-circulating-in-the-czech-republic-and-slovakia/613 "2021-02-11T21:35:11Z")
B.1.258∆, a SARS-CoV-2 variant with ∆H69/∆V70 in the Spike protein circulating in the Czech Republic and Slovakia Broňa Brejová1,\* , Viktória Hodorová2, Kristína Boršová3,4, Viktória Čabanová3, Lenka Reizigová5,6, Evan … --- ## [Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2](https://virological.org/t/tracking-the-international-spread-of-sars-cov-2-lineages-b-1-1-7-and-b-1-351-501y-v2/592)
**Author:** [@aine.otoole](https://virological.org/u/aine.otoole)\ **Replies:** 0\ **Last updated:** [January 13, 2021, 3:39pm UTC](https://virological.org/t/tracking-the-international-spread-of-sars-cov-2-lineages-b-1-1-7-and-b-1-351-501y-v2/592 "2021-01-13T15:39:24Z")
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 Áine O’Toole1,$,\*, Verity Hill1\*, Oliver G. Pybus2, Alexander Watts3,4, Isaac I. Bogoch5,6, Kamran Khan3,4,5, Jane P. Messina7, The CO… --- ## [Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings](https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586)
**Author:** [@nuno\_faria](https://virological.org/u/nuno_faria)\ **Replies:** 1\ **Last updated:** [January 25, 2021, 2:55am UTC](https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586 "2021-01-25T02:55:13Z")
Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings Nuno R. Faria1,2,3, Ingra Morales Claro3,4, Darlan Candido2,3, Lucas A. Moyses Franco3,4, Pamela S. Andrade3,4, Thais M. Coletti3… --- ## [Spatio-temporal heterogeneity and the spread of lineage B.1.1.7 in the United Kingdom](https://virological.org/t/spatio-temporal-heterogeneity-and-the-spread-of-lineage-b-1-1-7-in-the-united-kingdom/601)
**Author:** [@moritz.kraemer](https://virological.org/u/moritz.kraemer)\ **Replies:** 1\ **Last updated:** [January 20, 2021, 10:47am UTC](https://virological.org/t/spatio-temporal-heterogeneity-and-the-spread-of-lineage-b-1-1-7-in-the-united-kingdom/601 "2021-01-20T10:47:07Z")
THIS WORK HAS NOT BEEN PEER REVIEWED Spatio-temporal heterogeneity and the spread of lineage B.1.1.7 in the United Kingdom Moritz U.G. Kraemer1+, Verity Hill2\*, Christopher Ruis3\*, Kris V. Parag4, Anya Lindstrom Battle… --- ## [Phylogenetic evidence that B.1.1.7 has been circulating in the United States since early- to mid-November](https://virological.org/t/phylogenetic-evidence-that-b-1-1-7-has-been-circulating-in-the-united-states-since-early-to-mid-november/598)
**Author:** [@worobey](https://virological.org/u/worobey)\ **Replies:** 0\ **Last updated:** [January 19, 2021, 2:21am UTC](https://virological.org/t/phylogenetic-evidence-that-b-1-1-7-has-been-circulating-in-the-united-states-since-early-to-mid-november/598 "2021-01-19T02:21:06Z")
Phylogenetic evidence that B.1.1.7 has been circulating in the United States since early- to mid-November Brendan B. Larsen,1, Michael Worobey1\* 1Department of Ecology and Evolutionary Biology, University of Arizona \*C… --- ## [Detection of non-B.1.1.7 Spike ∆69/70 sequences (B.1.375) in the United States](https://virological.org/t/detection-of-non-b-1-1-7-spike-69-70-sequences-b-1-375-in-the-united-states/587)
**Author:** [@andersonbrito](https://virological.org/u/andersonbrito)\ **Replies:** 1\ **Last updated:** [January 14, 2021, 8:20pm UTC](https://virological.org/t/detection-of-non-b-1-1-7-spike-69-70-sequences-b-1-375-in-the-united-states/587 "2021-01-14T20:20:15Z")
Detection of non-B.1.1.7 Spike ∆69/70 sequences (B.1.375) in the United States We currently caution against using TaqPath S dropout as a proxy for B.1.1.7 in the US Gage Moreno1, Katarina Braun2, Brendan B. Larsen3, T… --- ## [Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020](https://virological.org/t/spike-e484k-mutation-in-the-first-sars-cov-2-reinfection-case-confirmed-in-brazil-2020/584)
**Author:** [@paola](https://virological.org/u/paola)\ **Replies:** 0\ **Last updated:** [January 10, 2021, 7:27pm UTC](https://virological.org/t/spike-e484k-mutation-in-the-first-sars-cov-2-reinfection-case-confirmed-in-brazil-2020/584 "2021-01-10T19:27:05Z")
Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil Authors Paola Cristina Resende1\*, João Felipe Bezerra2, Romero Henrique Teixeira de Vasconcelos2, Ighor Arantes3, Luciana Appolinario1, … --- ## [Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil](https://virological.org/t/spike-e484k-mutation-in-the-first-sars-cov-2-reinfection-case-confirmed-in-brazil/582)
**Author:** [@paola](https://virological.org/u/paola)\ **Replies:** 0\ **Last updated:** [January 10, 2021, 4:20pm UTC](https://virological.org/t/spike-e484k-mutation-in-the-first-sars-cov-2-reinfection-case-confirmed-in-brazil/582 "2021-01-10T16:20:44Z")
(topic withdrawn by author, will be automatically deleted in 24 hours unless flagged) --- ## [Updated Nextstain SARS-CoV-2 clade naming strategy](https://virological.org/t/updated-nextstain-sars-cov-2-clade-naming-strategy/581)
**Author:** [@trvrb](https://virological.org/u/trvrb)\ **Replies:** 0\ **Last updated:** [January 5, 2021, 6:52pm UTC](https://virological.org/t/updated-nextstain-sars-cov-2-clade-naming-strategy/581 "2021-01-05T18:52:07Z")
Trevor Bedford, Emma B Hodcroft, Richard A Neher The emerging 501Y.V1 and 501Y.V2 variants have pushed the Nextstrain team to revise our strategy for Nextstrain clade labels. Here, we propose a backwards-compatible upda… --- ## [Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data](https://virological.org/t/transmission-of-sars-cov-2-lineage-b-1-1-7-in-england-insights-from-linking-epidemiological-and-genetic-data/576)
**Author:** [@arambaut](https://virological.org/u/arambaut)\ **Replies:** 1\ **Last updated:** [December 30, 2020, 10:51pm UTC](https://virological.org/t/transmission-of-sars-cov-2-lineage-b-1-1-7-in-england-insights-from-linking-epidemiological-and-genetic-data/576 "2020-12-30T22:51:49Z")
Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data Erik Volz1\*+, Swapnil Mishra1\*, Meera Chand4\*, Jeffrey C. Barrett5\*, Robert Johnson1\*, Lily Geidelberg1, Wes R… --- ## [Lineage-specific growth of SARS-CoV-2 B.1.1.7 during the English national lockdown](https://virological.org/t/lineage-specific-growth-of-sars-cov-2-b-1-1-7-during-the-english-national-lockdown/575)
**Author:** [@moritz.gerstung](https://virological.org/u/moritz.gerstung)\ **Replies:** 1\ **Last updated:** [December 30, 2020, 10:19pm UTC](https://virological.org/t/lineage-specific-growth-of-sars-cov-2-b-1-1-7-during-the-english-national-lockdown/575 "2020-12-30T22:19:25Z")
Lineage-specific growth of SARS-CoV-2 B.1.1.7 during the English national lockdown Preliminary report. Harald Vöhringer1, Matthew Sinnott2, Roberto Amato2, Inigo Martincorena2, Dominic Kwiatkowski2, Jeffrey C. Barrett2 … --- ## [Detection of SARS-CoV-2 P681H Spike Protein Variant in Nigeria](https://virological.org/t/detection-of-sars-cov-2-p681h-spike-protein-variant-in-nigeria/567)
**Author:** [@pauloluniyi](https://virological.org/u/pauloluniyi)\ **Replies:** 0\ **Last updated:** [December 23, 2020, 6:08pm UTC](https://virological.org/t/detection-of-sars-cov-2-p681h-spike-protein-variant-in-nigeria/567 "2020-12-23T18:08:22Z")
Background Rambaut et al. published a report on the 19th of December 2020 describing a preliminary genomic characterization of an emergent SARS-CoV-2 lineage (B.1.1.7) in the United Kingdom and emphasized the need for a… --- ## [Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations](https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563)
**Author:** [@arambaut](https://virological.org/u/arambaut)\ **Replies:** 4\ **Last updated:** [December 21, 2020, 1:13am UTC](https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 "2020-12-21T01:13:58Z")
Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations Report written by: Andrew Rambaut1, Nick Loman2, Oliver Pybus3, Wendy Barclay4, Jeff Barrett5, Al… --- ## [Genomic epidemiology of the early stages of SARS-CoV-2 outbreak in Russia](https://virological.org/t/genomic-epidemiology-of-the-early-stages-of-sars-cov-2-outbreak-in-russia/531)
**Author:** [@g.bazykin](https://virological.org/u/g.bazykin)\ **Replies:** 6\ **Last updated:** [December 8, 2020, 1:51am UTC](https://virological.org/t/genomic-epidemiology-of-the-early-stages-of-sars-cov-2-outbreak-in-russia/531 "2020-12-08T01:51:44Z")
Russia ranks fourth in the number of confirmed COVID-19 cases globally. In our new preprint, we perform the first (to my knowledge) study of the genomic epidemiology of SARS-CoV-2 in Russia in March-April. This is based … --- ## [Genomic epidemiology of hCoV-19 in Guangdong Province, China](https://virological.org/t/genomic-epidemiology-of-hcov-19-in-guangdong-province-china/432)
**Author:** [@OliverPybus](https://virological.org/u/OliverPybus)\ **Replies:** 0\ **Last updated:** [March 9, 2020, 10:16pm UTC](https://virological.org/t/genomic-epidemiology-of-hcov-19-in-guangdong-province-china/432 "2020-03-09T22:16:39Z")
With the exception of Hubei Province, Guangdong Province in southern China has the highest number of recorded COVID-19 cases in the country. Guangdong Province and the Pearl River Delta Metropolitan Region comprise one o… --- ## [SARS-CoV-2 spatial structure 2: New evidence from RNA and protein sequences](https://virological.org/t/sars-cov-2-spatial-structure-2-new-evidence-from-rna-and-protein-sequences/532)
**Author:** [@ljones](https://virological.org/u/ljones)\ **Replies:** 0\ **Last updated:** [July 22, 2020, 8:25pm UTC](https://virological.org/t/sars-cov-2-spatial-structure-2-new-evidence-from-rna-and-protein-sequences/532 "2020-07-22T20:25:06Z")
This is a continuation of a previous post. We have reworked the clustering approach. We noticed a few k-mer distances could have been over-estimated due to sequencing differences at the genomes’ extremes. This did not a… --- ## [Genomic epidemiology of early introductions of SARS-CoV-2 into the Canadian province of Québec](https://virological.org/t/genomic-epidemiology-of-early-introductions-of-sars-cov-2-into-the-canadian-province-of-quebec/553)
**Author:** [@jesse.shapiro](https://virological.org/u/jesse.shapiro)\ **Replies:** 0\ **Last updated:** [September 18, 2020, 2:00pm UTC](https://virological.org/t/genomic-epidemiology-of-early-introductions-of-sars-cov-2-into-the-canadian-province-of-quebec/553 "2020-09-18T14:00:12Z")
Carmen Lia Murall (1)\*, Eric Fournier (2)\*, Jose Hector Galvez (3,4), Sarah J. Reiling (3,6), Pierre-Olivier Quirion (3,4,5), Anne-Marie Roy (3,6), Shu-Huang Chen (3,6), Paul Stretenowich (3,4), Mathieu Bourgey (3,4), Ma… --- ## [SARS-CoV-2 genomic epidemiology in Sierra Leone](https://virological.org/t/sars-cov-2-genomic-epidemiology-in-sierra-leone/544)
**Author:** [@johnatsandi](https://virological.org/u/johnatsandi)\ **Replies:** 0\ **Last updated:** [August 26, 2020, 1:49pm UTC](https://virological.org/t/sars-cov-2-genomic-epidemiology-in-sierra-leone/544 "2020-08-26T13:49:46Z")
We report the first 11 SARS-CoV-2 genomes from Sierra Leone, showing evidence of multiple importations and community transmission in the country. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiolog… --- ## [How many imports of virus from Asian and Europe into USA?](https://virological.org/t/how-many-imports-of-virus-from-asian-and-europe-into-usa/529)
**Author:** [@Brian\_Foley](https://virological.org/u/Brian_Foley)\ **Replies:** 0\ **Last updated:** [July 19, 2020, 10:58pm UTC](https://virological.org/t/how-many-imports-of-virus-from-asian-and-europe-into-usa/529 "2020-07-19T22:58:24Z")
An interesting question that can be explored with the thousands of complete genomes sampled in the USA, Europe, Asia etc. is “How many introductions were there into the USA, or into Italy, etc.?” I have seen some blog … --- ## [Phylogenetic analysis of SARS-CoV-2 in DRC](https://virological.org/t/phylogenetic-analysis-of-sars-cov-2-in-drc/528)
**Author:** [@aine.otoole](https://virological.org/u/aine.otoole)\ **Replies:** 0\ **Last updated:** [July 17, 2020, 9:02am UTC](https://virological.org/t/phylogenetic-analysis-of-sars-cov-2-in-drc/528 "2020-07-17T09:02:53Z")
Recent as of 2020-05-26, 127 SARS-CoV-2 genome sequences had been made available globally on GISAID providing insight into the diversity and dynamics of SARS-CoV-2 in the Democratic Republic of the Congo (DRC). The sampl… --- ## [Spike protein D614G variant paper published in Cell today](https://virological.org/t/spike-protein-d614g-variant-paper-published-in-cell-today/526)
**Author:** [@Brian\_Foley](https://virological.org/u/Brian_Foley)\ **Replies:** 2\ **Last updated:** [July 3, 2020, 1:45am UTC](https://virological.org/t/spike-protein-d614g-variant-paper-published-in-cell-today/526 "2020-07-03T01:45:32Z")
Our paper was published in Cell today: DOI:https://doi.org/10.1016/j.cell.2020.06.043 https://www.cell.com/cell/fulltext/S0092-8674(20)30820-5 A paper using different methods just went up on the bioRxiv which conclu… --- ## [Preliminary analysis of SARS-CoV-2 importation & establishment of UK transmission lineages](https://virological.org/t/preliminary-analysis-of-sars-cov-2-importation-establishment-of-uk-transmission-lineages/507)
**Author:** [@OliverPybus](https://virological.org/u/OliverPybus)\ **Replies:** 6\ **Last updated:** [June 26, 2020, 3:20pm UTC](https://virological.org/t/preliminary-analysis-of-sars-cov-2-importation-establishment-of-uk-transmission-lineages/507 "2020-06-26T15:20:31Z")
This work has been significantly updated and released as a preprint: https://www.medrxiv.org/content/10.1101/2020.10.23.20218446v1 Preliminary analysis of SARS-CoV-2 importation & establishment of UK transmission lineag… --- ## [Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil](https://virological.org/t/genomic-surveillance-of-sars-cov-2-reveals-community-transmission-of-a-major-lineage-during-the-early-pandemic-phase-in-brazil/514)
**Author:** [@paola](https://virological.org/u/paola)\ **Replies:** 0\ **Last updated:** [June 11, 2020, 3:33pm UTC](https://virological.org/t/genomic-surveillance-of-sars-cov-2-reveals-community-transmission-of-a-major-lineage-during-the-early-pandemic-phase-in-brazil/514 "2020-06-11T15:33:38Z")
Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil Paola Cristina Resende 1a, Edson Delatorre 2, Tiago Gräf 3, Daiana Mir 4, Fernando do Couto … --- ## [Introduction and spread of SARS-CoV-2 in the greater Boston area](https://virological.org/t/introduction-and-spread-of-sars-cov-2-in-the-greater-boston-area/503)
**Author:** [@lemieux](https://virological.org/u/lemieux)\ **Replies:** 0\ **Last updated:** [June 4, 2020, 8:15pm UTC](https://virological.org/t/introduction-and-spread-of-sars-cov-2-in-the-greater-boston-area/503 "2020-06-04T20:15:12Z")
Introduction and spread of SARS-CoV-2 in the greater Boston area Massachusetts has been severely impacted by the COVID-19 pandemic, with 101,592 cases and 7,152 deaths as of June 3, 2020. Seventy percent of the state’s … --- ## [Testing recombination in the pandemic SARS-CoV-2 strains](https://virological.org/t/testing-recombination-in-the-pandemic-sars-cov-2-strains/492)
**Author:** [@sergei.pond](https://virological.org/u/sergei.pond)\ **Replies:** 0\ **Last updated:** [May 28, 2020, 1:50am UTC](https://virological.org/t/testing-recombination-in-the-pandemic-sars-cov-2-strains/492 "2020-05-28T01:50:12Z")
Hongru Wang, Sergei L Kosakovsky Pond, Anton Nekrutenko, and Rasmus Nielsen Live version of this document is at Testing recombination in the pandemic SARS-CoV-2 strains / Sergei Pond | Observable To test whether ther… --- ## [Common Microdeletions in SARS-CoV-2 Sequences](https://virological.org/t/common-microdeletions-in-sars-cov-2-sequences/485)
**Author:** [@briannac](https://virological.org/u/briannac)\ **Replies:** 0\ **Last updated:** [May 15, 2020, 2:32pm UTC](https://virological.org/t/common-microdeletions-in-sars-cov-2-sequences/485 "2020-05-15T14:32:57Z")
Common Microdeletions in SARS-CoV-2 Sequences Brianna Sierra Chrisman 1, Kelley Paskov 2, Nate Stockham 3, Jae-Yoon Jung 2, Maya Varma4, Peter Washington1, Dennis P. Wall 2,5 correspondance: briannac@stanford.edu or dpw… --- ## [Early phylodynamics analysis of the COVID-19 epidemics in France using 194 genomes - April 10, 2020](https://virological.org/t/early-phylodynamics-analysis-of-the-covid-19-epidemics-in-france-using-194-genomes-april-10-2020/467)
**Author:** [@samuel.alizon](https://virological.org/u/samuel.alizon)\ **Replies:** 3\ **Last updated:** [April 29, 2020, 10:15am UTC](https://virological.org/t/early-phylodynamics-analysis-of-the-covid-19-epidemics-in-france-using-194-genomes-april-10-2020/467 "2020-04-29T10:15:34Z")
Early phylodynamics analysis of the COVID-19 epidemics in France 21-Apr-2020 Gonché Danesh, Baptiste Elie and Samuel Alizon ETE Modelling group, MIVEGEC, CNRS, IRD, Université de Montpellier Introduction This report … --- ## [Phylodynamic Analysis | 176 genomes | 6 Mar 2020](https://virological.org/t/phylodynamic-analysis-176-genomes-6-mar-2020/356)
**Author:** [@arambaut](https://virological.org/u/arambaut)\ **Replies:** 13\ **Last updated:** [April 2, 2020, 7:45am UTC](https://virological.org/t/phylodynamic-analysis-176-genomes-6-mar-2020/356 "2020-04-02T07:45:30Z")
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… --- ## [Phylogeography with whole genomes 24 Mar 2020](https://virological.org/t/phylogeography-with-whole-genomes-24-mar-2020/444)
**Author:** [@samantha\_lycett](https://virological.org/u/samantha_lycett)\ **Replies:** 0\ **Last updated:** [March 24, 2020, 9:07am UTC](https://virological.org/t/phylogeography-with-whole-genomes-24-mar-2020/444 "2020-03-24T09:07:55Z")
Like most of you I (Sam Lycett), and my undergraduate project student (Rhys Inward) have also been processing the GISAID data, especially now that there are ‘local’ sequences from Glasgow and Edinburgh (many many thanks … [Previous page](https://virological.org/c/novel-2019-coronavirus/ncov-2019-genomic-epidemiology/36.md) [Next page](https://virological.org/c/novel-2019-coronavirus/ncov-2019-genomic-epidemiology/36.md?page=2)