Schema for Nextstrain Clades - Nextstrain year-letter clade designations (19A, 19B, 20A, etc.)
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Database: wuhCor1 Primary Table: nextstrainClade Data last updated: 2024-04-06
Big Bed File Download: /gbdb/wuhCor1/nextstrain/nextstrainClade.bb Item Count: 38 The data is stored in the binary BigBed format.
Format description: Clades assigned by nextstrain.org
field | example | description |
chrom | NC_045512v2 | Reference sequence accession | chromStart | 0 | Start position in reference | chromEnd | 29903 | End position in reference | name | 19A | Name of clade | score | 0 | Placeholder for BED compatibility (0) | strand | . | Placeholder for BED compatibility (+) | thickStart | 0 | Start of where display should be thick | thickEnd | 0 | End of where display should be thick | reserved | 216,216,216 | itemRgb color | blockCount | 2 | Number of blocks (characteristic variants) | blockSizes | 1,1 | Comma separated list of block sizes | chromStarts | 0,29902 | Start positions relative to chromStart | variants | | Mutations that occurred on the path from the reference to this clade | dateInferred | | Date of clade branch inferred by TreeTime | dateConfMin | | Earliest date in TreeTime confidence interval | dateConfMax | | Latest date in TreeTime confidence interval | countryInferred | | Country inferred by TreeTime | countryConf | | Top-scoring countries and confidence from TreeTime | sampleCount | 56 | Number of samples belonging to the clade | samples | Wuhan-Hu-1/2019|Dec26, OL549280|Dec31, Wuhan/WIV07/2019|Dec30, Wuhan/WIV05/2019|Dec30, CHN/IQTC03/2020|Jan29, CHN/IQTC02/2020|Jan29, CHN/SH01/2020|Feb2, CHN/HZ-638/2020|Jan25, Wuhan/WH03/2020|Jan1, Mesocricetusauratus/HKG/15_P2/2020|May15, OM065369|Feb5, USA/CA-CDC-03039618-001/2020|Jan29, OM065340|Jan24, Wuhan/WIV06/2019|Dec30, CHN/HZ-90/2020|Jan21, Hangzhou/HZ-1/2020|Jan20, CHN/GZMU0031/2020|Feb25, KOR/KCDC12/2020|Feb1, CHN/SH-P69-C-3-Shanghai/2020|Feb19, CHN/P6-SARS-CoV-2/2020|Jan28, CHN/P2-SARS-CoV-2/2020|Jan17, CHN/P8-SARS-CoV-2/2020|Jan26, CHN/P7-SARS-CoV-2/2020|Jan27, CHN/Wuhan_YB012602/2020|Jan26, CHN/Wuhan_YB012611/2020|Jan26, OM065339|Jan22, OM065380|Feb8, OM065378|Feb7, KAZ/NCB-1/2020|Mar20, GEO/MM202082/2020|Feb28, GEO/Tb-7851/2020|May1, IRN/HGRC-2-2162/2020|Mar26, IRN/COVID19-IRVSH3/2020|May1, TLS/TL25/2020|Mar30, CHN/OS5/2020|Mar24, POL/PL_MCB_10/2020|Apr7, Iceland/13/2020|Feb27, CHN/Fuyang_FY002/2020|Mar10, CHN/OS1/2020|Mar24, CHN/Changzhou_JS27/2020|Jan26, OM065347|Jan29, Mesocricetusauratus/HKG/8_P2/2020|May15, IND/nimh-4263/2020|Apr23, TWN/CGMH-CGU-26/2020|Apr19, IND/GMCKN443/2020|Mar16, IND/GMC-RR1191/2020|Mar25, MYS/NC337/2020|Mar18, CHN/GZMU0030/2020|Feb27, CHN/HZ-477/2020|Jan24, OM065360|Feb2, FIN/1/2020|Jan29, CHN/Hefei-9/2020|Jan24, CHN/SH-P60-2-Unclear/2020|Feb12, AUS/SA03/2020|Jan30, AUS/SA02/2020|Jan30, CHN/SH-P212-A-2-Wuhan/2020|Jan29 | Samples belonging to the clade |
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Sample Rows
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chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | variants | dateInferred | dateConfMin | dateConfMax | countryInferred | countryConf | sampleCount | samples |
NC_045512v2 | 0 | 29903 | 19A | 0 | . | 0 | 0 | 216,216,216 | 2 | 1,1 | 0,29902 | | | | | | | 56 | Wuhan-Hu-1/2019|Dec26, OL549280|Dec31, Wuhan/WIV07/2019|Dec30, Wuhan/WIV05/2019|Dec30, CHN/IQTC03/2020|Jan29, CHN/IQTC02/2020|Ja ... |
NC_045512v2 | 0 | 29903 | 19B | 0 | . | 8781 | 28144 | 209,209,209 | 4 | 1,1,1,1 | 0,8781,28143,29902 | C8782T, T28144C (ORF8:L84S) | 2019-12-30 | 2019-12-30 | 2019-12-30 | | | 36 | BEL/GHB-03021/2020|Feb3, CHN/Yunnan-01/2020|Jan17, CHN/Wuhan_IME-WH01/2019|Dec30, ESP/Valencia5/2020|Feb27, CHN/IQTC04/2020|Jan2 ... |
NC_045512v2 | 0 | 29903 | 20A | 0 | . | 240 | 23403 | 202,202,202 | 6 | 1,1,1,1,1,1 | 0,240,3036,14407,23402,29902 | C3037T; C241T, A23403G (S:D614G); C14408T (ORF1b:P314L) | 2020-01-26 | 2020-01-11 | 2020-02-14 | | | 93 | CMR/CENT308695/2020|Mar26, AUS/NT13/2020|Mar25, BEN/197/2020|Mar15, Switzerland/BS-UHB-42341001/2020|Jul6, OX420865|Aug31, CMR/D ... |
NC_045512v2 | 0 | 29903 | 20B | 0 | . | 240 | 28883 | 195,195,195 | 9 | 1,1,1,1,1,1,1,1,1 | 0,240,3036,14407,23402,28880,28881,28882,29902 | C3037T; C241T, A23403G (S:D614G); C14408T (ORF1b:P314L); G28881A (N:R203K), G28882A (N:R203K), G28883C (N:G204R) | 2020-02-23 | 2020-01-03 | 2020-02-24 | | | 111 | NGA/CV-1/2020|Feb27, USA/KS-QDX-3424/2020|Jul13, CHN/SH-P179-4-Asia-India/2020|Jun21, CHN/MY-001/2020|Mar10, LBN/LB-R9/2020|Mar1 ... |
NC_045512v2 | 0 | 29903 | 20C | 0 | . | 240 | 25563 | 188,188,188 | 8 | 1,1,1,1,1,1,1,1 | 0,240,1058,3036,14407,23402,25562,29902 | C3037T; C241T, A23403G (S:D614G); C14408T (ORF1b:P314L); G25563T (ORF3a:Q57H); C1059T (ORF1a:T265I) | 2020-03-03 | 2019-12-27 | 2020-03-14 | | | 24 | ISR/NH_MA_0727/2020|Jul27, TUN/TUN_ADAGE_5004/2020|Jul9, CHN/SH-P178-4-North-America-Canada/2020|Jun22, Argentina/UW21010209251/ ... |
NC_045512v2 | 0 | 29903 | 20D | 0 | . | 240 | 28883 | 181,181,181 | 13 | 1,1,1,1,1,1,1,1,1,1,1,1,1 | 0,240,3036,4001,10096,13535,14407,23402,23730,28880,28881,28882,29902 | C3037T; C241T, A23403G (S:D614G); C14408T (ORF1b:P314L); G28881A (N:R203K), G28882A (N:R203K), G28883C (N:G204R); C4002T (ORF1a: ... | 2020-03-21 | 2020-03-16 | 2020-03-21 | | | 15 | ZAF/NHLS-UCT-GS-0046/2020|Mar22, PRY/WOR12903A609_202103267_2-4710520/2020|Mar22, SouthAfrica/NHLS-UCT-LA-9010/2020|Mar21, EGY/P ... |
NC_045512v2 | 0 | 29903 | 20E | 0 | . | 240 | 29645 | 0,0,0 | 13 | 1,1,1,1,1,1,1,1,1,1,1,1,1 | 0,240,444,3036,6285,14407,21254,22226,23402,26800,28931,29644,29902 | C3037T; C241T, A23403G (S:D614G); C14408T (ORF1b:P314L); C28932T (N:A220V); T445C, C6286T, G21255C, C22227T (S:A222V), C26801G, ... | 2020-08-21 | 2020-05-19 | 2020-10-29 | | | 3 | SRB/NSNIVNS4-12-11/2020|Nov12, Switzerland/NE-ETHZ-550437/2020|Dec7, Denmark/DCGC-117200/2021|Jan4 |
NC_045512v2 | 0 | 29903 | 20F | 0 | . | 240 | 28883 | 167,167,167 | 15 | 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 | 0,240,1162,3036,7539,14407,16646,18554,22991,23400,23402,28880,28881,28882,29902 | C3037T; C241T, A23403G (S:D614G); C14408T (ORF1b:P314L); G28881A (N:R203K), G28882A (N:R203K), G28883C (N:G204R); A1163T (ORF1a: ... | 2020-07-02 | 2020-07-02 | 2020-07-02 | Australia | | 1 | AUS/NT51/2020|Jul2 |
NC_045512v2 | 0 | 29903 | 20G | 0 | . | 240 | 28869 | 160,160,160 | 15 | 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 | 0,240,1058,3036,10318,14407,18423,21303,23402,25562,25906,27963,28471,28868,29902 | C3037T; C241T, A23403G (S:D614G); C14408T (ORF1b:P314L); G25563T (ORF3a:Q57H); C1059T (ORF1a:T265I); C10319T (ORF1a:L3352F), C27 ... | 2020-06-15 | 2020-05-22 | 2020-06-25 | | | 8 | USA/AK-PHL620/2020|Jun25, NZL/21CV0048/2021|Jan7, USA/IN-CDC-2-3903673/2021|Feb5, USA/JFZR/2020|Dec3, USA/IA-CDC-LC0000341/2020| ... |
NC_045512v2 | 0 | 29903 | 20H (Beta) | 0 | . | 173 | 28887 | 0,0,0 | 29 | 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 | 0,173,240,1058,3036,5229,10322,14407,21800,22282,22283,22284,22285,22286,22287,22288,22289,22290,22812,23011,23062,23402,23663,2 ... | C3037T; C241T, A23403G (S:D614G); C14408T (ORF1b:P314L); G25563T (ORF3a:Q57H); C1059T (ORF1a:T265I); A10323G (ORF1a:K3353R); G17 ... | 2020-08-22 | 2020-05-28 | 2020-10-15 | | | 16 | ZAF/NHLS-UCT-GS-1314/2020|Nov2, MWI/MLW001038/2021|Jan11, PHL/COVID-74873/2021|Jul3, HongKong/HKPU-00176/2021|Feb27, TZA/KIDH-01 ... |
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Nextstrain Clades (nextstrainClade) Track Description
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Description
Nextstrain.org displays
data about mutations that occur in the current 2019/2020 outbreak.
Nextstrain has a powerful user interface for viewing the timestamped molecular phylogeny tree
that it infers from the patterns of mutations in sequences worldwide using the
TreeTime algorithm.
Nextstrain defines clades named by year and letter, anticipating that SARS-CoV-2 will
become a seasonal virus in the coming years. For more information about the rationale
and properties of current clades, see
https://github.com/nextstrain/ncov/blob/master/docs/src/reference/naming_clades.md.
The Nextstrain Mutations track contains all mutations shown on Nextstrain,
of which this track's mutations are a very small subset.
Methods
Nextstrain downloads SARS-CoV-2 genomes from
GISAID
as they are submitted by labs worldwide.
Nextstrain identifies mutations that define clades of interest and puts them in the file
clades.tsv.
The genome sequences and metadata including clades.tsv are processed by an
automated pipeline
and annotations are written to a data file
that UCSC downloads and extracts annotations for display.
Data Access
You can download the bigBed file underlying this track (nextstrainClade.bb) from our
Download Server. The data can be explored interactively with the
Table Browser
or the Data Integrator. The data can also be
accessed from scripts through our API.
Credits
Thanks to
nextstrain.org for
sharing its analysis of genomes collected by
GISAID,
and to researchers worldwide for sharing their SARS-CoV-2 genome sequences.
References
Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher
RA.
Nextstrain: real-time tracking of pathogen evolution.
Bioinformatics. 2018 Dec 1;34(23):4121-4123.
PMID: 29790939; PMC: PMC6247931
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