# nCoV-2019 Genomic Epidemiology **URL:** https://virological.org/c/novel-2019-coronavirus/ncov-2019-genomic-epidemiology/36.md?page=2 [Latest](https://virological.org/latest.md) · [Categories](https://virological.org/categories.md) **Page:** 3 --- ## [Response to “On the origin and continuing evolution of SARS-CoV-2”](https://virological.org/t/response-to-on-the-origin-and-continuing-evolution-of-sars-cov-2/418)
**Author:** [@oscar.maclean](https://virological.org/u/oscar.maclean)\ **Replies:** 11\ **Last updated:** [March 16, 2020, 4:26pm UTC](https://virological.org/t/response-to-on-the-origin-and-continuing-evolution-of-sars-cov-2/418 "2020-03-16T16:26:15Z")
Response to “On the origin and continuing evolution of SARS-CoV-2” Oscar A. MacLean\*, Richard Orton, Joshua B. Singer, David L. Robertson. MRC-University of Glasgow Centre for Virus Research (CVR). \*To whom correspond… --- ## [Phylodynamic Analyses of outbreaks in China, Italy, Washington State (USA), and the Diamond Princess](https://virological.org/t/phylodynamic-analyses-of-outbreaks-in-china-italy-washington-state-usa-and-the-diamond-princess/439)
**Author:** [@tanja.stadler](https://virological.org/u/tanja.stadler)\ **Replies:** 1\ **Last updated:** [March 13, 2020, 7:26pm UTC](https://virological.org/t/phylodynamic-analyses-of-outbreaks-in-china-italy-washington-state-usa-and-the-diamond-princess/439 "2020-03-13T19:26:50Z")
Phylodynamic Analyses of outbreaks in China, Italy, Washington State (USA), and the Diamond Princess Insights on the R0, the number of cases through time, and the time of epidemic origin Timothy G. Vaughan1,2, Sarah A. … --- ## [Phylodynamic analysis of a densely sampled COVID19 outbreak in Weifang, China](https://virological.org/t/phylodynamic-analysis-of-a-densely-sampled-covid19-outbreak-in-weifang-china/436)
**Author:** [@erik.volz](https://virological.org/u/erik.volz)\ **Replies:** 0\ **Last updated:** [March 10, 2020, 12:54pm UTC](https://virological.org/t/phylodynamic-analysis-of-a-densely-sampled-covid19-outbreak-in-weifang-china/436 "2020-03-10T12:54:30Z")
Phylodynamic analysis of a densely sampled COVID19 outbreak in Weifang, China Erik M Volz, Han Fu 1 , Haowei Wang 1 , Xiaoyue Xi 2 , Wei Chen 3 , Dehui Liu 3 , Yingying Chen 3 , Mengmeng Tian 3 , Wei Tan 4 , Junjie Zai 5… --- ## [\[Update 2\] Evolutionary & epidemiological analysis of 128 genomes](https://virological.org/t/update-2-evolutionary-epidemiological-analysis-of-128-genomes/423)
**Author:** [@tanja.stadler](https://virological.org/u/tanja.stadler)\ **Replies:** 0\ **Last updated:** [March 6, 2020, 2:23pm UTC](https://virological.org/t/update-2-evolutionary-epidemiological-analysis-of-128-genomes/423 "2020-03-06T14:23:16Z")
Phylodynamic analyses based on 128 sequences Jérémie Sciré1,2, Timothy G. Vaughan1,2, Sarah A. Nadeau1,2, and Tanja Stadler1,2,\* 1Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland 2Swiss … --- ## [Phylodynamic analysis of SARS-CoV-2 | Update 2020-03-06](https://virological.org/t/phylodynamic-analysis-of-sars-cov-2-update-2020-03-06/420)
**Author:** [@verity.hill](https://virological.org/u/verity.hill)\ **Replies:** 0\ **Last updated:** [March 6, 2020, 11:59am UTC](https://virological.org/t/phylodynamic-analysis-of-sars-cov-2-update-2020-03-06/420 "2020-03-06T11:59:48Z")
Phylogenetic analysis of SARS-CoV-2 genomes 06-Mar-2020 Verity Hill and Andrew Rambaut, University of Edinburgh, Edinburgh, UK verity.hill@ed.ac.uk,a.rambaut@ed.ac.uk This is a brief report following previous Virolog… --- ## [Phylodynamic Analyses based on 11 genomes from the Italian outbreak](https://virological.org/t/phylodynamic-analyses-based-on-11-genomes-from-the-italian-outbreak/426)
**Author:** [@tanja.stadler](https://virological.org/u/tanja.stadler)\ **Replies:** 0\ **Last updated:** [March 6, 2020, 5:05pm UTC](https://virological.org/t/phylodynamic-analyses-based-on-11-genomes-from-the-italian-outbreak/426 "2020-03-06T17:05:53Z")
Phylodynamic Analyses based on 11 genomes from the Italian outbreak Insights on the R0, the number of cases through time, and the time of epidemic origin Jérémie Sciré1,2, Timothy G. Vaughan1,2, Sarah A. Nadeau1,2, and … --- ## [\[Update\] Evolutionary & epidemiological analysis of 128 genomes](https://virological.org/t/update-evolutionary-epidemiological-analysis-of-128-genomes/413)
**Author:** [@tanja.stadler](https://virological.org/u/tanja.stadler)\ **Replies:** 0\ **Last updated:** [March 4, 2020, 4:41pm UTC](https://virological.org/t/update-evolutionary-epidemiological-analysis-of-128-genomes/413 "2020-03-04T16:41:06Z")
We updated our previous analysis of 93 genomes (Evolutionary & epidemiological analysis of 93 genomes) with 35 additional sequences. ​ Evolutionary analysis ​ We performed an evolutionary analysis to quantify the cloc… --- ## [Evolutionary & epidemiological analysis of 93 genomes](https://virological.org/t/evolutionary-epidemiological-analysis-of-93-genomes/405)
**Author:** [@tanja.stadler](https://virological.org/u/tanja.stadler)\ **Replies:** 1\ **Last updated:** [February 27, 2020, 3:20pm UTC](https://virological.org/t/evolutionary-epidemiological-analysis-of-93-genomes/405 "2020-02-27T15:20:42Z")
We performed an evolutionary & epidemiological analysis of 93 genomes as described in the attached pdf. We are looking forward to read your feedback! Jeremie Scire, Tim Vaughan, Tanja Stadler 2020-02-25 report ScireVa… --- ## [How close are we to the 'phylodynamic threshold'? A simulation study](https://virological.org/t/how-close-are-we-to-the-phylodynamic-threshold-a-simulation-study/372)
**Author:** [@erik.volz](https://virological.org/u/erik.volz)\ **Replies:** 0\ **Last updated:** [January 31, 2020, 5:00pm UTC](https://virological.org/t/how-close-are-we-to-the-phylodynamic-threshold-a-simulation-study/372 "2020-01-31T17:00:43Z")
tl;dr: Almost there. Brush off your phylodynamic models. Previous reports here and here and here and here have shown that current sequences on GISAID and Genbank allow preliminary conclusions to be drawn about TMRCA … --- ## [Phylodynamic estimation of incidence and prevalence of novel coronavirus (nCoV) infections through time](https://virological.org/t/phylodynamic-estimation-of-incidence-and-prevalence-of-novel-coronavirus-ncov-infections-through-time/391)
**Author:** [@trvrb](https://virological.org/u/trvrb)\ **Replies:** 2\ **Last updated:** [February 14, 2020, 2:31am UTC](https://virological.org/t/phylodynamic-estimation-of-incidence-and-prevalence-of-novel-coronavirus-ncov-infections-through-time/391 "2020-02-14T02:31:31Z")
This post is mirrored from https://github.com/blab/ncov-phylodynamics. I was liking GitHub for this as it allows analysis to be versioned. But would love to have discussion in this thread. Phylodynamic estimation of inc… --- ## [Number of mutations along a transmission chain](https://virological.org/t/number-of-mutations-along-a-transmission-chain/371)
**Author:** [@john.mccrone](https://virological.org/u/john.mccrone)\ **Replies:** 0\ **Last updated:** [January 31, 2020, 4:23pm UTC](https://virological.org/t/number-of-mutations-along-a-transmission-chain/371 "2020-01-31T16:23:43Z")
Time, mutations, and transmissions There have been a number of interesting posts, here and on twitter, discussing the time scale of the current 2019-nCoV tree, and what we can and can’t infer from the genetic data given… --- ## [Sequencing technology and sequence variation in nCoV-2019](https://virological.org/t/sequencing-technology-and-sequence-variation-in-ncov-2019/374)
**Author:** [@james\_hereward](https://virological.org/u/james_hereward)\ **Replies:** 0\ **Last updated:** [February 2, 2020, 10:39am UTC](https://virological.org/t/sequencing-technology-and-sequence-variation-in-ncov-2019/374 "2020-02-02T10:39:43Z")
Hi there, I’m not a virologist but I was interested to have a quick look and see if there were any noticeable biases in the sequencing technology used for the nCoV-2019 genome sequences available at GISAID. Four differe… --- ## [Temporal signal and the evolutionary rate of 2019 n-CoV using 47 genomes collected by Feb 01 2020](https://virological.org/t/temporal-signal-and-the-evolutionary-rate-of-2019-n-cov-using-47-genomes-collected-by-feb-01-2020/379)
**Author:** [@sebastian.duchene](https://virological.org/u/sebastian.duchene)\ **Replies:** 4\ **Last updated:** [February 5, 2020, 4:11pm UTC](https://virological.org/t/temporal-signal-and-the-evolutionary-rate-of-2019-n-cov-using-47-genomes-collected-by-feb-01-2020/379 "2020-02-05T16:11:46Z")
Sebastian Duchene (sduchene@unimelb.edu.au) Leo Featherstone (leo.featherstone@unimelb.edu.au) Melina Haritopoulou-Sinanidou (melhs99@gmail.com) Peter Doherty Institute for Infection and Immunity University of Melbou… --- ## [SARS comparison](https://virological.org/t/sars-comparison/376)
**Author:** [@arambaut](https://virological.org/u/arambaut)\ **Replies:** 1\ **Last updated:** [February 3, 2020, 8:26pm UTC](https://virological.org/t/sars-comparison/376 "2020-02-03T20:26:49Z")
This is an analysis of 15 SARS genomes from early 2003. This is all of the SARS genomes I could find for which I could obtain or make a good guess at the date of collection. Figure 1 | Maximum likelihood tree under GT… --- ## [Genome sequences by date and location](https://virological.org/t/genome-sequences-by-date-and-location/380)
**Author:** [@arambaut](https://virological.org/u/arambaut)\ **Replies:** 2\ **Last updated:** [February 3, 2020, 5:51pm UTC](https://virological.org/t/genome-sequences-by-date-and-location/380 "2020-02-03T17:51:12Z")
Genome sequences as of 02/02/2020. Dots represent date of collection of the sample. Colour by location of case. --- ## [Phylodynamic analysis of nCoV-2019 genomes – 29-Jan-2020](https://virological.org/t/phylodynamic-analysis-of-ncov-2019-genomes-29-jan-2020/353)
**Author:** [@arambaut](https://virological.org/u/arambaut)\ **Replies:** 1\ **Last updated:** [January 29, 2020, 4:35pm UTC](https://virological.org/t/phylodynamic-analysis-of-ncov-2019-genomes-29-jan-2020/353 "2020-01-29T16:35:18Z")
This post has been updated with new data here: http://virological.org/t/phylodynamic-analysis-44-genomes-29-jan-2020/356/2 --- ## [Phylogenetic analysis of 23 nCoV-2019 genomes, 2020-01-23](https://virological.org/t/phylogenetic-analysis-of-23-ncov-2019-genomes-2020-01-23/335)
**Author:** [@arambaut](https://virological.org/u/arambaut)\ **Replies:** 6\ **Last updated:** [January 28, 2020, 1:39pm UTC](https://virological.org/t/phylogenetic-analysis-of-23-ncov-2019-genomes-2020-01-23/335 "2020-01-28T13:39:46Z")
Phylogenetic analysis of nCoV-2019 genomes 23-Jan-2020 Andrew Rambaut, University of Edinburgh, Edinburgh UK a.rambaut@ed.ac.uk This post has been updated with new data here: http://virological.org/t/phylodynamic-a… --- ## [Clock and TMRCA based on 27 genomes](https://virological.org/t/clock-and-tmrca-based-on-27-genomes/347)
**Author:** [@Kristian\_Andersen](https://virological.org/u/Kristian_Andersen)\ **Replies:** 5\ **Last updated:** [January 28, 2020, 4:43am UTC](https://virological.org/t/clock-and-tmrca-based-on-27-genomes/347 "2020-01-28T04:43:02Z")
Estimates of the clock and TMRCA for 2019-nCoV based on 27 genomes January 25, 2020 Kristian Andersen, Scripps Research kristian@andersen-lab.com Following up on the analyses provided by Andrew Rambaut this is a brie… --- ## [Further musings on the tMRCA](https://virological.org/t/further-musings-on-the-tmrca/340)
**Author:** [@OliverPybus](https://virological.org/u/OliverPybus)\ **Replies:** 5\ **Last updated:** [January 27, 2020, 11:13am UTC](https://virological.org/t/further-musings-on-the-tmrca/340 "2020-01-27T11:13:13Z")
Louis du Plessis and I have written a short report of our calculations. They use the same logic as the estimates Richard Neher shared on Twitter, with a couple of extensions. CAVEAT: The number of sequences and mutation… --- ## [Epidemiological Data from the nCoV-2019 Outbreak: Early Descriptions from Publicly Available Data](https://virological.org/t/epidemiological-data-from-the-ncov-2019-outbreak-early-descriptions-from-publicly-available-data/337)
**Author:** [@moritz.kraemer](https://virological.org/u/moritz.kraemer)\ **Replies:** 2\ **Last updated:** [January 25, 2020, 5:45pm UTC](https://virological.org/t/epidemiological-data-from-the-ncov-2019-outbreak-early-descriptions-from-publicly-available-data/337 "2020-01-25T17:45:37Z")
Epidemiological data from the 2019 nCoV outbreak: early descriptions We have collected publicly available information on cases confirmed during the ongoing nCoV-2019 outbreak. Data were entered in a spreadsheet with eac… --- ## [Preliminary phylogenetic analysis of 11 nCoV2019 genomes, 2020-01-19](https://virological.org/t/preliminary-phylogenetic-analysis-of-11-ncov2019-genomes-2020-01-19/329)
**Author:** [@arambaut](https://virological.org/u/arambaut)\ **Replies:** 1\ **Last updated:** [January 20, 2020, 3:25pm UTC](https://virological.org/t/preliminary-phylogenetic-analysis-of-11-ncov2019-genomes-2020-01-19/329 "2020-01-20T15:25:23Z")
This is a brief report outlining some phylogenetic analysis of the initial genome sequences. It gives some preliminary findings for information purposes is not intended for publication as an academic work. All the data u… [Previous page](https://virological.org/c/novel-2019-coronavirus/ncov-2019-genomic-epidemiology/36.md?page=1)