Virus Mutations Reveal How COVID-19 Really Spread

Genetic sequences of the coronavirus tell story of when the virus arrived in each country and where it came from.

Our graphic in Scientific American's Graphic Science section in the June 2020 issue shows a phylogenetic tree based on a snapshot of the data model from Nextstrain as of 31 March 2020.

▲ Virus Mutations Reveal How COVID-19 Really Spread. Text by Mark Fischetti (Senior Editor), art direction by Jen Christiansen (Senior Graphics Editor), source: Nextstrain (enabled by data from GISAID).

Cover of Nature Cancer April 2020

Our design on the cover of Nature Cancer's April 2020 issue shows mutation spectra of patients from the POG570 cohort of 570 individuals with advanced metastatic cancer.

▲ Each ellipse system represents the mutation spectrum of an individual patient. Individual ellipses in the system correspond to the number of base changes in a given class and are layered by mutation count. Ellipse angle is controlled by the proportion of mutations in a class within the sample and its size is determined by a sigmoid mapping of mutation count scaled within the layer. The opacity of each system represents the duration since the diagnosis of advanced disease. (read more)

The cover design accompanies our report in the issue Pleasance, E., Titmuss, E., Williamson, L. et al. (2020) Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes. Nat Cancer 1:452–468.

Modeling infectious epidemics

Every day sadder and sadder news of its increase. In the City died this week 7496; and of them, 6102 of the plague. But it is feared that the true number of the dead this week is near 10,000 ....
—Samuel Pepys, 1665

This month, we begin a series of columns on epidemiological models. We start with the basic SIR model, which models the spread of an infection between three groups in a population: susceptible, infected and recovered.

▲ Nature Methods Points of Significance column: Modeling infectious epidemics. (read)

We discuss conditions under which an outbreak occurs, estimates of spread characteristics and the effects that mitigation can play on disease trajectories. We show the trends that arise when "flattenting the curve" by decreasing `R_0`.

▲ Nature Methods Points of Significance column: Modeling infectious epidemics. (read)

This column has an interactive supplemental component that allows you to explore how the model curves change with parameters such as infectious period, basic reproduction number and vaccination level.

▲ Nature Methods Points of Significance column: Modeling infectious epidemics. (Interactive supplemental materials)

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.

The Outbreak Poems

I'm writing poetry daily to put my feelings into words more often during the COVID-19 outbreak.

That moment
when
you know a moment.

Branch to branch,
flit,
look everywhere,
chirp.

Memory,
scent
of thought fleeting.

Distant pasts
all
ways in plural
form.

Read the poems and learn what a piku is.

Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses

A poster full of epidemiological worry and statistics. Now updated with the genome of SARS-CoV-2 and COVID-19 case statistics as of 3 March 2020.

▲ Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses (zoom)

Bacterial and viral genomes of various diseases are drawn as paths with color encoding local GC content and curvature encoding local repeat content. Position of the genome encodes prevalence and mortality rate.

The deadly genomes collection has been updated with a posters of the genomes of SARS-CoV-2, the novel coronavirus that causes COVID-19.

▲ Genomes of 56 SARS-CoV-2 coronaviruses that causes COVID-19.

▲ Ball of 56 SARS-CoV-2 coronaviruses that causes COVID-19.

▲ The first SARS-CoV-2 genome (MT019529) to be sequenced appears first on the poster.

Using Circos in Galaxy Australia Workshop

A workshop in using the Circos Galaxy wrapper by Hiltemann and Rasche. Event organized by Australian Biocommons.

▲ Using Circos in Galaxy Australia workshop. (zoom)

Download workshop slides.

Galaxy wrapper training materials, Saskia Hiltemann, Helena Rasche, 2020 Visualisation with Circos (Galaxy Training Materials).