Schema for Nextstrain Clades - Nextstrain year-letter clade designations (19A, 19B, 20A, etc.)
  Database: wuhCor1    Primary Table: nextstrainClade Data last updated: 2021-10-19
Big Bed File: /gbdb/wuhCor1/nextstrain/nextstrainClade.bb
Item Count: 21
Format description: Clades assigned by nextstrain.org
fieldexampledescription
chromNC_045512v2Reference sequence accession
chromStart0Start position in reference
chromEnd29903End position in reference
name19AName of clade
score0Placeholder for BED compatibility (0)
strand.Placeholder for BED compatibility (+)
thickStart0Start of where display should be thick
thickEnd0End of where display should be thick
reserved61,21,199itemRgb color
blockCount2Number of blocks (characteristic variants)
blockSizes1,1Comma separated list of block sizes
chromStarts0,29902Start positions relative to chromStart
variantsMutations that occurred on the path from the reference to this clade
dateInferredDate of clade branch inferred by TreeTime
dateConfMinEarliest date in TreeTime confidence interval
dateConfMaxLatest date in TreeTime confidence interval
countryInferredCountry inferred by TreeTime
countryConfTop-scoring countries and confidence from TreeTime
sampleCount65Number of samples belonging to the clade
samplesWuhan-Hu-1/2019|Wuhan-Hu-1/2019|Dec26, Wuhan/WH01/2019|Wuhan/WH01/2019|Dec26, AUS/SA01/2020|AUS/SA01/2020|Jan30, AUS/SA04/2020|AUS/SA04/2020|Jan30, IND/29/2020|IND/29/2020|Jan27, AUS/VIC14/2020|AUS/VIC14/2020|Feb2, NPL/61-TW/2020|NPL/61-TW/2020|Jan13, USA/MA-CDC-MA1/2020|USA/MA-CDC-MA1/2020|Jan29, Mesocricetusauratus/HKG/13_P2/2020|Mesocricetusauratus/HKG/13_P2/2020|May15, Japan/DP0476/2020|Japan/DP0476/2020|Feb16, KAZ/NCB-1/2020|KAZ/NCB-1/2020|Mar20, IRN/HGRC-1.1-IPI-8206/2020|IRN/HGRC-1.1-IPI-8206/2020|Mar9, TWN/CGMH-CGU-21/2020|TWN/CGMH-CGU-21/2020|Feb29, GEO/Tb-7851/2020|GEO/Tb-7851/2020|May1, NZL/20VR0174/2020|NZL/20VR0174/2020|Feb27, IRN/12624/2020|IRN/12624/2020|Apr28, IRN/COVID19-IRVSH3/2020|IRN/COVID19-IRVSH3/2020|May1, LC594644|LC594644|Mar19, NZL/20CV0306/2020|NZL/20CV0306/2020|Mar30, NZL/20VR3025/2020|NZL/20VR3025/2020|Mar23, MYS/188407/2020|MYS/188407/2020|Mar18, PAK/JRCGR-KHI46/2020|PAK/JRCGR-KHI46/2020|May3, MYS/IIUM316/2020|MYS/IIUM316/2020|Apr9, TLS/TL21/2020|TLS/TL21/2020|Apr14, GUM/GU-NHG-03/2020|GUM/GU-NHG-03/2020|Mar20, IND/nimh-1454/2020|IND/nimh-1454/2020|Apr15, PHL/GS/2020|PHL/GS/2020|Apr3, GMB/GC19-026/2020|GMB/GC19-026/2020|Mar21, IND/OUMRK1090/2020|IND/OUMRK1090/2020|Mar25, CHN/Hefei-909/2020|CHN/Hefei-909/2020|Mar2, AUS/NT04/2020|AUS/NT04/2020|Feb22, AUS/NT01/2020|AUS/NT01/2020|Feb21, ITA/INMI2-N/2020|ITA/INMI2-N/2020|Jan30, GEO/MM202054/2020|GEO/MM202054/2020|Feb27, Iceland/13/2020|Iceland/13/2020|Feb27, KOR/2020-CoV55_Nasopharynx/2020|KOR/2020-CoV55_Nasopharynx/2020|Feb26, KOR/KCDC31-NCCP43342/2020|KOR/KCDC31-NCCP43342/2020|Jul28, AUS/VIC186/2020|AUS/VIC186/2020|Mar19, GRC/52_37266/2020|GRC/52_37266/2020|Apr1, NZL/20VR1763/2020|NZL/20VR1763/2020|Mar25, NZL/20VR1785/2020|NZL/20VR1785/2020|Mar26, USA/OSPHL01362/2020|USA/OSPHL01362/2020|Apr22, JOR/SEARCH-0056-JOR/2020|JOR/SEARCH-0056-JOR/2020|Mar17, TLS/TL25/2020|TLS/TL25/2020|Mar30, AUS/TAS72/2020|AUS/TAS72/2020|Mar17, BRA/SP02cc/2020|BRA/SP02cc/2020|Mar18, BRA/SP02/2020|BRA/SP02/2020|Feb28, OU815144|OU815144|Mar25, VNM/nCoV-19-01S/2020|VNM/nCoV-19-01S/2020|Jan22, Finland/FIN-1-VE6-P4/2020|Finland/FIN-1-VE6-P4/2020|Jan29, TWN/CGMH-CGU-01/2020|TWN/CGMH-CGU-01/2020|Jan25, USA/IL-CDC-IL1/2020|USA/IL-CDC-IL1/2020|Jan21, Iceland/1448/2020|Iceland/1448/2020|Mar25, KOR/KCDC12-NCCP43330/2020|KOR/KCDC12-NCCP43330/2020|Mar17, Netherlands/Loon_op_zand_1363512/2020|Netherlands/Loon_op_zand_1363512/2020|Feb29, HongKong/HKPU-00041/2020|HongKong/HKPU-00041/2020|Apr4, SWE/01/2020|SWE/01/2020|Feb7, THA/SI200383-NT/2020|THA/SI200383-NT/2020|Jan23, HongKong/HKPU-00028/2020|HongKong/HKPU-00028/2020|Feb11, AUS/VIC03/2020|AUS/VIC03/2020|Jan25, EGY/EGY_CCHE57357_A_27/2020|EGY/EGY_CCHE57357_A_27/2020|Jul5, AUS/NT42/2020|AUS/NT42/2020|May1, DEU/BavPat8-ChVir1356/2020|DEU/BavPat8-ChVir1356/2020|Feb3, FRA/BavPat1/2020|FRA/BavPat1/2020|Apr20, DEU/BavPat3-ChVir1020/2020|DEU/BavPat3-ChVir1020/2020|Jan28Samples belonging to the clade

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsvariantsdateInferreddateConfMindateConfMaxcountryInferredcountryConfsampleCountsamples
NC_045512v202990319A0.0061,21,19921,10,2990265Wuhan-Hu-1/2019|Wuhan-Hu-1/2019|Dec26, Wuhan/WH01/2019|Wuhan/WH01/2019|Dec26, AUS/SA01/2020|AUS/SA01/2020|Jan30, AUS/SA04/2020|A ...
NC_045512v202990319B0.87812814456,72,23041,1,1,10,8781,28143,29902C8782T, T28144C (ORF8:L84S)2020-01-102020-01-082020-01-1261GBR/DMSOp13.5/2020|GBR/DMSOp13.5/2020|Jan29, THA/SI205457-NST/2020|THA/SI205457-NST/2020|Mar16, KHM/Kunming_kms-2/2020|KHM/Kunmi ...
NC_045512v202990320A0.2402340364,124,22361,1,1,1,1,10,240,3036,14407,23402,29902A23403G (S:D614G); C241T; C3037T; C14408T (ORF1b:P314L)2020-01-242020-01-142020-01-26241PER/covper095/2020|PER/covper095/2020|Apr1, NZL/20CV0278/2020|NZL/20CV0278/2020|Mar24, TUR/KOC-IST-SP3/2020|TUR/KOC-IST-SP3/2020 ...
NC_045512v202990320B0.2402888380,163,19091,1,1,1,1,1,1,1,10,240,3036,14407,23402,28880,28881,28882,29902A23403G (S:D614G); C241T; C3037T; C14408T (ORF1b:P314L); G28881A (N:R203K), G28882A (N:R203K), G28883C (N:G204R)2020-02-202020-02-192020-02-20245SAU/KAIMRC67/2020|SAU/KAIMRC67/2020|Apr1, LR963386|LR963386|May1, USA/GA-CDC-2742/2020|USA/GA-CDC-2742/2020|Feb29, PER/Peru-10/2 ...
NC_045512v202990320C0.24025563103,189,14781,1,1,1,1,1,1,10,240,1058,3036,14407,23402,25562,29902A23403G (S:D614G); C241T; C3037T; C14408T (ORF1b:P314L); G25563T (ORF3a:Q57H); C1059T (ORF1a:T265I)2020-02-272020-02-262020-02-27115NZL/20CV0325/2020|NZL/20CV0325/2020|Apr2, ISR/hCov-19-Israel-CVL-n-6136/2020|ISR/hCov-19-Israel-CVL-n-6136/2020|Mar15, LR963466| ...
NC_045512v202990320D0.24028883132,206,108131,1,1,1,1,1,1,1,1,1,1,1,10,240,3036,4001,10096,13535,14407,23402,23730,28880,28881,28882,29902A23403G (S:D614G); C241T; C3037T; C14408T (ORF1b:P314L); G28881A (N:R203K), G28882A (N:R203K), G28883C (N:G204R); C4002T (ORF1a: ...2020-03-122020-03-052020-03-1961PAK/SARS-CoV-2_89/2020|PAK/SARS-CoV-2_89/2020|Apr15, PER/covper043/2020|PER/covper043/2020|May5, PER/covper050/2020|PER/covper05 ...
NC_045512v202990320E (EU1)0.24029645171,201,81131,1,1,1,1,1,1,1,1,1,1,1,10,240,444,3036,6285,14407,21254,22226,23402,26800,28931,29644,29902A23403G (S:D614G); C241T; C3037T; C14408T (ORF1b:P314L); C26801G; T445C, C6286T, G21255C, C22227T (S:A222V), C28932T (N:A220V), ...2020-05-122020-04-092020-06-1417TUN/TUN-202019695/2020|TUN/TUN-202019695/2020|Jul12, TUN/TUN-202063686/2020|TUN/TUN-202063686/2020|Dec1, Canislupusfamiliaris/IT ...
NC_045512v202990320F0.24028883211,204,64151,1,1,1,1,1,1,1,1,1,1,1,1,1,10,240,1162,3036,7539,14407,16646,18554,22991,23400,23402,28880,28881,28882,29902A23403G (S:D614G); C241T; C3037T; C14408T (ORF1b:P314L); G28881A (N:R203K), G28882A (N:R203K), G28883C (N:G204R); A1163T (ORF1a: ...2020-06-082020-05-242020-06-2415AUS/VIC2397/2020|AUS/VIC2397/2020|Jun30, AUS/VIC15589/2020|AUS/VIC15589/2020|Oct2, AUS/TAS278/2020|AUS/TAS278/2020|Jul19, AUS/GC ...
NC_045512v202990320G0.24028869242,185,54151,1,1,1,1,1,1,1,1,1,1,1,1,1,10,240,1058,3036,10318,14407,18423,21303,23402,25562,25906,27963,28471,28868,29902A23403G (S:D614G); C241T; C3037T; C14408T (ORF1b:P314L); G25563T (ORF3a:Q57H); C1059T (ORF1a:T265I); C27964T (ORF8:S24L); C10319 ...2020-06-212020-05-042020-07-1455USA/NMDOH-2020616315/2020|USA/NMDOH-2020616315/2020|Dec12, USA/MA-MGH-02992/2020|USA/MA-MGH-02992/2020|Jul14, USA/IA-CDC-ASC2100 ...
NC_045512v202990320H (Beta, V2)0.173288870,0,0391,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,10,173,240,1058,3036,5229,10322,11287,11288,11289,11290,11291,11292,11293,11294,11295,14407,21800,22205,22282,22283,22284,22285,2 ...A23403G (S:D614G); C241T; C3037T; C14408T (ORF1b:P314L); G25563T (ORF3a:Q57H); C1059T (ORF1a:T265I); A10323G (ORF1a:K3353R); T11 ...2020-09-102020-05-212020-10-2936Pakistan/UHS2-Pak-411/2021|Pakistan/UHS2-Pak-411/2021|Jul22, USA/NC-CDC-STM-000046977/2021|USA/NC-CDC-STM-000046977/2021|Mar30, ...

Nextstrain Clades (nextstrainClade) Track Description
 

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