Dataset
ncov
global
Date Range
Use this slider to filter the data based on the sample date. This may include inferred dates for ancestral nodes in the tree, and thus the date range here can be wider than the sample collection range.
2019-12-21
2021-01-15
Color By
Change the metadata field which the visualisation is coloured by.
The phylogeny, map and frequencies panel (if available) will all be coloured in a consistent fashion.
Clade
Filter Data
Use this box to filter the displayed data based upon filtering criteria. For instance, start typing a country's name to filter the data accordingly.
Data is filtered by forming a union of selected values within each category, and then taking the intersection between categories (if more than one category is selected).
Scroll to the bottom of the main page (under the data visualisation) to see an expanded display of filters and available values.
Type filter query here...
Currently selected filter categories:
1 x country
The visible data is being filtered by this
Remove this filter
Tree Options
Change various options relating to how the tree is displayed. The exact options available depend on the dataset and specific analysis performed.
If Branch Length is available, you can choose to display the tree branches in terms of (nucleotide) divergence or (inferred) time. It is often helpful to toggle on confidence intervals to guage the uncertainty in the reconstruction of internal node dates.
Layout
Branch Length
Branch Labels
clade
Tip Labels
Sample Name
Second Tree
Select...
Map Options
Change various options relating to how the map is displayed.
The geographic resolution chooses the metadata values which define where samples are placed on the map. This can be the same as the selected color-by but is often not!
Geographic resolution
country
Frequency Options
Normalize frequencies controls whether the vertical axis represents the entire dataset or only the samples currently visible (e.g. due to filtering).
Animation Options
Change various options relating to how the animation proceeds.
Animation Speed

Panel Options
Control which panels are being displayed and whether to show the tree and the map side-by-side (grid) or expanded (full).
Note that what options are available here are dataset specific!
Language
English
Genomic epidemiology of novel coronavirus - Global subsampling
avatarMaintained by the Nextstrain team. Enabled by data from gisaid-logo
Showing 23 of 3953 genomes sampled between Jan 2020 and Jan 2021. Filtered to
Japan (23)
The visible data is being filtered by this
Inactivate this filter
Remove this filter
.
Phylogeny
19A19A19B19B20B20B20J/501Y.V320J/501Y.V3Clade2019-Dec2020-Jan2020-Feb2020-Mar2020-Apr2020-May2020-Jun2020-Jul2020-Aug2020-Sep2020-Oct2020-Nov2020-Dec2021-Jan2021-FebDateJapan/TY-WK-012/2020Japan/PG-0237/2020Japan/DP0724/2020Japan/PG-0291/2020Japan/Donner36/2020Japan/PG-0528/2020Japan/NGY-NNH-054/2020Japan/Donner53/2020Japan/Donner39/2020Japan/NGY-NNH-050/2020Japan/NGY-NNH-051/2020Japan/NGY-NNH-055/2020Japan/Donner59/2020Japan/PG-0483/2020Japan/NGY-NNH-053/2020Japan/YCU02/2020Japan/Donner93/2020Japan/NGY-NNH-049/2020Japan/NGY-NNH-052/2020Japan/IC-0564/2021Japan/IC-0561/2021Japan/IC-0562/2021Japan/IC-0563/202119A19B20A20E (EU1)20C20G20H/501Y.V220B20D20I/501Y.V120J/501Y.V320F
Geography
19A19A19B19B20B20B20J/501Y.V320J/501Y.V3Clade
Diversity
MNORF1aORF1bORF3aORF7aORF8SMNORF1aORF1bORF3aS0.00.20.40.602,0004,0006,0008,00010,00012,00014,00016,00018,00020,00022,00024,00026,00028,00002,0004,0006,0008,00010,00012,00014,00016,00018,00020,00022,00024,00026,00028,000
Frequencies (colored by Clade and normalized to 100% at each time point for 23 out of a total of 3953 tips)
20J/501Y.V320B19B19A2020-Jan2020-Feb2020-Mar2020-Apr2020-May2020-Jun2020-Jul2020-Aug2020-Sep2020-Oct2020-Nov2020-Dec2021-Jan2021-Feb0%20%40%60%80%100%
Data updated 2021-01-13Auspice v2.22.2
Powered by Nextstrain (Hadfield et al Bioinformatics)