Thanks to #opendata sharing via @GISAID, we've updated nextstrain.org/ncov/gisaid with 741778 new #COVID19 #SARSCoV2 sequences during the last month!

1/7
Thanks to all new submitters:

NPHL Cameroon, Southwest Hospital Ethiopia, @CerfigGuinee, @NUFeinbergMed, @comui2017, @ILRI, Institut Pasteur Maroc, Central Public Health Reference Lab of Sierra Leone, @PathCareSA1, @CSIR_NEIST, @iitdelhi, @DBEBtweeting

2/7
Molecular Solutions Care Health, @MedGenomeLabs, @BjgmcSgh, @IISERPune, @blalbiotech, @uphimpactslives, VenomCoV, @unsri, @DeepSeqNotts, @kmu1928, Nagasaki Institute of Environment and Public Health, Sendai City Institute of Public Health

3/7
Japan COVID-19 Open Data Consortium, @UTokyo_News_en, Royal Medical Services Jordan, @UKM_UMBI, Medical Research Institute Sri Lanka, @CreativeSoftLK, Kaohsiung Medical University, VG-CARE, Central Research Institute of Epidemiology Belarus

4/7
Institute of Public Health Bosnia and Herzegovina, Regional Hospital Liberec, University Hospital Pilsen, @UK_Muenster, @UMG_Tweet, Pharmgenetix, @UNI_FIRENZE, @NIPH_RKS, Institute of Public Health of Montenegro, @StichtingPAMM, @WSSEGorzowWlkp, HUGC Dr Negrin

5/7

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More from @nextstrain

9 Oct
We've just updated Nextstrain clade designations to partition clade 21A (corresponding to the Delta WHO variant) into subclades 21I and 21J following our previously defined rules for defining clades when mutational and frequency thresholds are met. 1/4 Image
Clade 21I is still a Delta variant virus, but possesses additional spike mutation A222V and ORF1a mutations P1640L, A3209V, V3718A and T3750I. 2/4 Image
Clade 21J is still a Delta variant virus, but possesses additional ORF1a mutations A1306S, P2046L, P2287S, V2930L, T3255I and T3646A, ORF7b mutation T40I, as well as N mutation G215C. Clade 21J is now the predominate form of Delta with an estimated ~79% global frequency. 3/4 Image
Read 4 tweets
11 Jun
We have just released a new version of the Nextclade web application clades.nextstrain.org for #SARSCOV2. We now use Nextalign (C++ via wasm) under the hood, which allows for many new exacting features!

A quick tour!

1/7
Analysis now takes a few seconds to start, but overall it has become much faster and analyzing hundreds of sequences should be no problem. You can download the reference alignments, including translations of SARS-CoV-2 genes, for further analyses.

2/7
You can now examine the diversity of the nucleotide alignment and alignments of different proteins. Select a gene from the drop-down or click on a gene in the genome annotation panel below.

3/7
Read 7 tweets
10 Jun
Thanks to #opendata sharing via @GISAID, we've updated nextstrain.org/ncov with 10836 new #COVID19 #SARSCoV2 sequences!

1/4
You can see new sequences from Australia, Guadeloupe and Mexico on nextstrain.org/ncov/oceania and nextstrain.org/ncov/north-ame….

(Thanks to @SAHealth, @JMPawlotsky, @APHP, @Inserm, @institutpasteur, @todoscicese)

2/4
Check out new sequences from Belarus, Singapore, Taiwan and Vietnam on nextstrain.org/ncov/europe and nextstrain.org/ncov/asia.

(Thanks to RRPCEM Belarus, @mysgh, @Taiwan_CDC, @OUCRU_Vietnam)

3/4
Read 4 tweets
6 Apr
Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 24322 new #COVID19 #SARSCoV2 sequences!

Check out new seqs from Togo (1) & Uganda (120) on nextstrain.org/ncov/africa.

(Thanks to @transvihmi, @ird_fr, @Inserm, @UVRIug, @MRC_Uganda, @LSHTM)

1/14
New sequences from Aruba (36), Bonaire (26), Brazil (368) and Curacao (30) can be found on nextstrain.org/ncov/south-ame….

(Thanks to @rivm, Instituto Adolfo Lutz, @hosp_einstein , @UFCSPA)

2/14
You can see the new sequences from Australia (24) and New Zealand (20) on nextstrain.org/ncov/oceania.

(Thanks to @NSWHPathology @WestSydHealth @Sydney_Uni PHV-FSS #PathWest Laboratory Medicine @WAHealth #CIDMPH @ESRNewZealand @MathStorey @Joepdl @sciolato)

3/14
Read 14 tweets
31 Mar
Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 9739 new #COVID19 #SARSCoV2 sequences!

Check out the new sequences from Australia (14) on nextstrain.org/ncov/oceania.

(Thanks to #RoyalPrinceAlfredHospital, PHV-FSS)

1/14
New sequences from Libya (76), Morocco (2) & Nigeria (1) can be seen on nextstrain.org/ncov/africa.

(Thanks to Genologica Málaga, Laboratoire de Recherche et d'Analyses Medicales de la Gendarmerie Royale, @NCDCgov)

2/14
Seqs from Argentina (769) & Brazil (3) on nextstrain.org/ncov/south-ame….

(Thanks to HRU @CadicUshuaia @UNTDF @intaCIAP Biocódices @gcba @CONICETDialoga @intaargentina LMBA @AcuarioRParana @ProyectoPAIS4, Laboratorio Central Mg. Luis Alfredo Pianciola @MinSaludNeuquen, @fiocruz)

3/14
Read 14 tweets
30 Mar
Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 11073 new #COVID19 #SARSCoV2 seqs!

New seqs from Australia (16) on nextstrain.org/ncov/oceania.

(Thanks to @NSWHPathology, @WestSydHealth, @Sydney_Uni, #PathWest Lab Med, @WAHealth, #CIDMPH)

1/9
Check out the new sequences from India (99), Indonesia (10) and Pakistan (12) on nextstrain.org/ncov/asia.

(Thanks to @icmr_niv, @DBTIndia, #NIMHANS, @DBT_NCCS_Pune, @ILS_Bhubaneswar, NIHRD Indonesia, @NIH_Pakistan)

2/9
You can find the new sequences from Belgium (834) and Czech Republic (100) on nextstrain.org/ncov/europe.

(Thanks to @az_delta @JessaZiekenhuis @umons @GroupeJolimont Rega Institute at @KU_Leuven @FNBrno Institute of Applied Biotechnologies)

3/9
Read 9 tweets

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