Based on their frequencies and rate of growth, we've designated 4 new Nextstrain clades from @PangoNetwork lineages:
23C (CH.1.1)
23D (XBB.1.9)
23E (XBB.2.3)
23F (EG.5.1)

1/9 23C (CH.1.1) is a sublineage of 22D (BA.2.75) with additional spike RBD mutations at 346T, 444T, 452R & 486S. This non-XBB lineage has persisted despite the dominance of XBB descendants.
Currently most prevalent in Australia & New Zealand, it is also growing in Europe.

2/9

Based on its rapid growth, particularly in Asia, we've designated the recombinant @PangoNetwork lineage XBB.1.16 & its descendants as clade 23B, labeled "23B (Omicron)" on Nextstrain trees.

Like 23A, 23B is a descendant of the recombinant 22F (XBB).

1/9 23B (XBB.1.16) is different from 22F (XBB) primarily through 3 new Spike mutations - S:E180V; S:K478R; & S:486P (acquired independently from other XBB sublineages).
In addition, S:G252V is inherited from ancestral XBB.1

https://twitter.com/firefoxx66/status/1648588097381101570

2/9

Based on its rapid growth in multiple geographies, we've designated the recombinant @PangoNetwork lineage XBB.1.5 & its descendants as clade 23A, labelled "23A (Omicron)" on Nextstrain trees.

23A (XBB.1.5) is a descendant of the recombinant 22F (XBB).

1/7 23A (XBB.1.5) is different from 22F (XBB) primarily through 2 new Spike muts - 1 in ancestor XBB.1 (S:G252V), & 1 in 23A itself S:486S -> S:486P. This 'P' change is associated with an increased ACE2 binding, which is likely why 23A is spreading.

https://twitter.com/firefoxx66/status/1611387923072417792

2/7

Based on its rapid growth in multiple geographies, we've designed the recombinant @PangoNetwork lineage XBB & its descendants as clade 22F, labelled "22F (Omicron)" on Nextstrain trees.

Because 22F is a recombinant, its phylogenetic placement doesn't reflect its history.

1/5 22F/XBB is the result of a recombination between BJ.1 (BA.2.10.1.1) & BM.1.1.1 (BA.2.75.3.1.1.1) with breakpoint in S1 (first part of spike).

Recombination occurs during co-infection with 2 different variants, when parts of two different genomes end up together.

2/5

Based on its rapid growth in multiple geographies, we've designed @PangoNetwork lineage BQ.1 and descendants (most notably BQ.1.1) as clade 22E, labelled as "22E (Omicron)" on Nextstrain trees.

1/4 Clade 22E (lineage BQ.1) has been growing in frequency at a rate of 0.11 per day in USA, which is equivalent to the initial growth of 22B (BA.5) in the US & UK.
5-15% of recent samples in the USA & many countries in Europe are 22E & it might soon dominate in some places.

2/4

Based on sustained logistic growth in frequency in India, we've designed @PangoNetwork lineage BA.2.75 as clade 22D, labeled as "22D (Omicron)" to denote it still being considered as "Omicron variant" by @WHO. 1/4 Lineage BA.2.75 / clade 22D has been growing in frequency at a rate of 0.12 per day in India, which is equivalent to initial growth of BA.5 in the US and the UK, and is now outcompeting BA.5 in India. 2/4

We have updated our #monkeypox build to include the latest #opendata sequences from @CDCgov from Maryland, Texas, Virginia, & Florida.

These sequences fall outside where most of the recent sequences cluster (blue).

nextstrain.org/monkeypox

1/6

https://twitter.com/HelenBranswell/status/1532742516755283975

The Maryland sequence (2021-11) is ancestral to most of the recently detected #monkeypox sequences, suggesting this lineage has likely been circulating in humans for months, if not longer.

It may offer hints about how mutations in this lineage have accumulated.

2/6

clades.nextstrain.org can now detect if sequences are potentially contaminated or are recombinants.

This is how it works:
Nextclade places sequences on a reference tree. Mutations relative to the nearest neighbor are identified (called private) and analyzed further 1/ These private mutations are split into three categories:

1) Reversions to reference.

2) Labeled: Mutations to a genotype that is common get labeled with the name of the clade the genotype is common in.

3) Unlabeled: Mutations that are neither reversions nor labeled. 2/

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 Clade 21I is still a Delta variant virus, but possesses additional spike mutation A222V and ORF1a mutations P1640L, A3209V, V3718A and T3750I. 2/4

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

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

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

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

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

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

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 48183 new #COVID19 #SARSCoV2 sequences!

New sequences from Côte d'Ivoire (33) and Kenya (5) can be seen on nextstrain.org/ncov/africa.

(Thanks to CHU Bouaké @KEMRI_Kenya @tagcc_info)

1/20 Check out the new seqs from Angola (71), Nigeria (11) and South Africa (276) on nextstrain.org/ncov/africa. Botswana (1) currently not visible due to random subsampling.

(Thanks to @BotsHarvard @NCDCgov @krisp_news @rjlessells @Tuliodna @EduanWilkinson @nicd_sa @BotsHarvard)

2/20

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 10924 new #COVID19 #SARSCoV2 sequences!

Check out the new sequences from Indonesia (1) and Singapore (7) on nextstrain.org/ncov/asia.

(Thanks to @upnjakarta, NCID NPHL Singapore)

1/10 New sequences from Botswana (2), Libya (1) and South Africa (4, currently not visible due to random subsampling) can be found on nextstrain.org/ncov/africa.

(Thanks to @BotsHarvard, Genologica Málaga, @nhls_sa, @nicd_sa)

2/10

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 11079 new #COVID19 #SARSCoV2 sequences!

You can find the new sequences from Brazil (38) and Chile (71) on nextstrain.org/ncov/south-ame….

(Thanks to @fiocruz, Instituto Adolfo Lutz, @ispch)

1/13 Check out the new sequences from Botswana (4), Burkina Faso (9), Rwanda (79) and Togo (1) on nextstrain.org/ncov/africa.

(Thanks to @BotsHarvard, @CentreMURAZ, @GIGA_ULiege, @transvihmi, @ird_fr, @Inserm)

2/13

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 2507 new #COVID19 #SARSCoV2 sequences!

Check out the new seqs from Ghana (13), Brazil (110) and Chile (3) below.

(Thanks to @UHASGhana, @hosp_einstein, Instituto Adolfo Lutz, @uandresbello)

1/7 @GISAID @UHASGhana @hosp_einstein @uandresbello Check out the new sequences from Belarus (25), Belgium (3), Finland (62), France (148) and Germany (93) on nextstrain.org/ncov/europe.

(Thanks to @ChariteBerlin @MedMicroLab_UA @helsinkiuni @TimoSmura @cerbaresearch @institutpasteur @HHU_de)

2/7

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 1847 new #COVID19 #SARSCoV2 sequences!

New sequences from Canada (47) can be found on nextstrain.org/ncov/north-ame….

(Thanks to @McMasterU)

1/5 @GISAID @McMasterU USA (1091) seqs on nextstrain.org/ncov/north-ame….

(Thanks to @QuestDX @cychiu98 @UofCalifornia @czbiohub @WeillCornell @HealthyFla @HealthNYGov @OHdeptofhealth @UtahDepOfHealth @Dr_KFO @ErinYoun @microbemagic1 Wyoming PHL @jacksonlab @r_tewhey @TexasDSHS @CAPublicHealth @CDPHE)

2/5

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 9358 new #COVID19 #SARSCoV2 sequences!

Check out the new sequences from Australia (91), Argentina (133) and Brazil (73) below.

(Thanks to PHV-FSS, @ANLIS_Malbran, @IEC_BR)

1/8 @GISAID @ANLIS_Malbran @IEC_BR You can see the new sequences from Bangladesh (3), China (6), India (8), Myanmar (8) and South Korea (335) on nextstrain.org/ncov/asia.

(Thanks to Genomic Research Lab at #BCSIR China CDC @ccmb_csir VRDL, Gandhi Medical College, MDRU-DHR, DSMRC Myanmar @KoreaCDC)

2/8