Thread by @wolfeagle1989

CoV-Spectrum has loaded new data. As expected, “Pirola” clan JN.1 (BA.2.86.1.1) is climbing on #Collection42 . JN.1 is still small, but growth rate estimates are not driven by a cluster. 1/cov-spectrum.org/collections/42

France has reported the most JN.1 sequences so far (9), but these are spread across 6 French Regions. Also, there are 27 known JN.1 sequences not the 16 found on CoV-Spectrum. 2 of the missing have mangled date information. 9 are too new to be in today’s CoV-Spectrum update. 2/2

Countries reporting JN.1 so far: Belgium (1), Denmark (2), UK/England (7), France (9), Germany (1), Ireland (1), Israel (1), Luxembourg (1), Netherlands (1), Spain (1), USA (2; 1 North Carolina and 1 New Jersey traveler from Israel). Note that this list will likely grow.

And France reported 3 more JN.1 earlier today for a total 12 JN.1 from France and 30 JN.1 worldwide.

3 JN.1 now reported from Iceland bringing the global JN.1 total to 33. These are the first 3 full JN.1 from Iceland.

Note: Following UShER I’m excluding a previous Icelandic near-JN.1 BA.2.86.1 that only missed the last JN.1 defining mutation (in ORF7b) but that had the critical S:L455S mutation. I acknowledge that reasonable people could disagree with this exclusion.

2 more JN.1 have now been reported in GISAID. 1 more from Israel, and 1 more from Netherlands.

My query (nucleotide mutations C18894T, T15756A, T27810C) now shows 35 JN.1 total in GISAID.

And yet 2 more JN.1 from France bringing the global JN.1 total to 37. These are the first JN.1 reported from Occitanie and Nouvelle-Acquitanie.

3 more French JN.1s. 2 Ile-de-France and 1 Grand Est. All with collection dates 2023-10-02. Global JN.1 total now 40.

2 JN.1 submitted 2023-10-16. 1 from Luxembourg and 1 from New Jersey, USA. 12 submitted so far today 2023-10-17. 8 France (3 regions), 4 England. Global JN.1 total now 54.

A 55th JN.1 sequence has been submitted. California, USA. This is the first JN.1 reported from western North America.

56th and 57th JN.1 sequences now known. Airport surveillance inbound traveler from UAE to New Jersey, USA. With the way US airport surveillance samples work, these are likely a pooled sample and an individual sample of a single case.

58th JN.1 sequence. 2nd JN.1 detection in California, USA.

59th and 60th JN.1 sequences. 2nd from Germany and 2nd from Spain.

61st JN.1 sequence. 2nd from Ireland. Note: 61 JN.1 is by my nucleotide query C18894T, T15756A, T27810C that requires the last JN.1-defining mutation ORF7b:F19L/T27810C. GISAID includes 2 more sequences. UShER calls several fewer based and misses an entire emerging branch.

Note: The issue with the UShER JN.1 calls is that UShER calls JN.1 only after synonymous nucleotide mutation C21610T, but this location toggles back and forth between T and C and looks like an artifact. As a result UShER also excludes much of the emerging JN.1+ORF1a:T170I branch.

A 62nd JN.1 now (by the query I’m using). This is the 3rd from California, USA.

63rd through 69th JN.1 sequences have appeared on GISAID. All are from France (which has been a JN.1 hotspot and which had not uploaded much this week.) These sequences are from 3 Regions of France all of which have previously reported JN.1 sequences.

A 70th JN.1 sequence has been submitted. This is the 3rd from Denmark.

A comment: In the 4 weeks of 2023-09-16 to 2023-10-13, France submitted 6555 sequences for an average of 1638.75 per week. For the week of 2023-10-14 to 2023-10-20, France has submitted 636 sequences but JN.1 was 2% of those sequences. So the global JN.1 total may be impacted.

71st and 72nd JN.1 sequences. 1st from Illinois, USA and 1st from Connecticut, USA. h/t @LongDesertTrain

@LongDesertTrain 73rd JN.1 sequence. 3rd from Israel (not counting the traveler from Israel previously detected in New Jersey, USA.)

@LongDesertTrain 74th JN.1 sequence. 12th from England.

@LongDesertTrain Now there is a 75th JN.1 sequence. It is the 1st from Wales.

@LongDesertTrain And a 76th JN.1 sequence. It is the 1st from Scotland.

@LongDesertTrain Some of the anticipated French data has finally appeared. 77th through 80th JN.1 on GISAID from France. 3rd and 4th from Auvergne-Rhône-Alps, 2nd from Nouvelle-Aquitaine, 2nd from Occitanie. Now 36 total from France.

@LongDesertTrain 81st through 83rd JN.1. All from Ontario, Canada. 1st 3 for Ontario and 1st 3 for Canada. h/t @RajlabN

@LongDesertTrain @RajlabN 84th JN.1 sequence. Texas, USA. 1st in Texas. 11th in USA. Additional note: Houston area.

@LongDesertTrain @RajlabN 20 more JN.1 from France plus 1 from Singapore (h/t @HNimanFC) for a global total of 105. For the French sequences, regions are 9 IDF, 6 GES, 2 HDF, 2 CVL, and 1 BFC. Total JN.1 from France 56. Total JN.1 by French regions with new JN.1: IDF 21, GES 11, HDF 8, BFC 4, 2 CVL.

@LongDesertTrain @RajlabN @HNimanFC And more JN.1. Global total 121. 2 more from England. Portugal enters with its first 14 JN.1.

@LongDesertTrain @RajlabN @HNimanFC 122nd JN.1. 1st from Bulgaria.

@LongDesertTrain @RajlabN @HNimanFC 123rd JN.1. 1st from Bretagne, France. 57th from France. 21st submitted from France today (2023-10-24). 25th from France this week. h/t @RajlabN

@LongDesertTrain @RajlabN @HNimanFC 124th JN.1. Virginia, USA. 12th USA. 1st Virginia.

@LongDesertTrain @RajlabN @HNimanFC 125th JN.1. Quebec, Canada. 1st Quebec. 4th Canada.

@LongDesertTrain @RajlabN @HNimanFC 126th JN.1. Liguria, Italy. 1st from Liguria and 1st from Italy.

@LongDesertTrain @RajlabN @HNimanFC 127th JN.1. Aragon, Spain. 1st from Aragon, 3rd from Spain. (Others from Spain were from Albacete and from Extremadura.)

@LongDesertTrain @RajlabN @HNimanFC 128th and 129th global JN.1 sequences. 1st and 2nd from Switzerland. 1 is from Geneva. 1 is from an unspecified canton.

@LongDesertTrain @RajlabN @HNimanFC 130th and 131th JN.1 sequences. Umbria, Italy and Nova Scotia, Canada. 1st from Umbria and 2nd from Italy. 1st from from Nova Scotia and 5th from Canada.

@LongDesertTrain @RajlabN @HNimanFC 11 new JN.1 sequences reported from Iceland. Total known JN.1 now 14 from Iceland and 142 globally.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma has found a 12th probable JN.1 in today’s upload from Iceland that is missing coverage at T27810 (ORF7b:F19). For consistency I plan to not include it and an older Icelandic sequence like it in my JN.1 counts, but I acknowledge reasonable people may disagree.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma 143rd JN.1 sequence (by my nucleotide mutation query). New Jersey, USA airport surveillance, traveler inbound from the UK. 13th USA, 5th New Jersey, 4th New Jersey airport surveillance, 3rd non-pooled New Jersey airport surveillance inbound traveler.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma 7 more JN.1. 4 Netherlands (3rd to 6th), 3rd Utrecht, 1st and 2nd Zuid-Holland, 1st Limburg. 2 Switzerland (3rd and 4th), 1st from Basel-Stadt and 1st from Wallis. 1 Belgium (2nd), 1st from Leuven.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma Global JN.1 total now 150 by my nucleotide query.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma 12 new JN.1 from Limerick, Ireland. Totals 13 Limerick, 14 Ireland, 162 global.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma Now 11 more JN.1 from France. 2 new from Auvergne-Rhône-Alpes (ARA; total 6), 3 new from Occitanie (OCC; total 5), 6 new from Provence-Alpes-Cote d’Azur (PAC; total 7). Total 68 from France. Global total 173.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma 2 more JN.1 from Vaud, Switzerland. 1st and 2nd from Vaud. 5th and 6th from Switzerland. Global total JN.1 175 by my query 175. And there appear to be a few JN.1 that my query misses.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma Oops that tweet had an incomplete edit. Global total JN.1 175 by my query.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma 5 more JN.1 from Denmark. Total 8 from Denmark. Global total 180 by the query I’ve been using which does find 1 JN.1/EG.5.1.1 recombinant found by @JosetteSchoenma and 2 other likely JN.1 sequences. h/t @siamosolocani

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani Correction: “which does *not* find”. The query I’m using does not find the JN.1/EG.5.1.1 recombinant or the 2 other likely JN.1 sequences.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 181st JN.1 sequence. Lombardy, Italy. 1st in Lombardy, 3rd in Italy.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 182nd JN.1 sequence. Chiba, Japan. 1st in Chiba, 1st in Japan. h/t @siamosolocani

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 183rd JN.1 sequence. Madrid, Spain. 1st from Madrid, 4th from Spain.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 184th JN.1 sequence. 2nd from Singapore.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 185th JN.1 sequence. West Flanders, Belgium. 1st in West Flanders, 3rd in Belgium.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 186th and 187th JN.1 sequences. Flemish Brabant and Brussels, Belgium. 2nd from Flemish Brabant and 1st from Brussels. 4th and 5th from Belgium.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 188th and 189th JN.1 sequences. 1st and 2nd from Castilla y Leon, Spain. 5th and 6th from Spain.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 190th and 191st JN.1 sequences. Both from California, USA. 4th and 5th from California. 14th and 15th from USA.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 192nd and 193rd JN.1 sequences. Both from Balearic Islands, Spain. 1st and 2nd from Balearic Islands. 7th and 8th from Spain.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 22 new JN.1 sequences from France. 2 CVF, 2 GES, 3 HDF, 11 IDF, 2 NOR, 2 PDL. Totals 90 France, 4 CVL, 13 GES, 11 HDF, 32 IDF, 3 NOR, 2 PDF. Global JN.1 total 215.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani Correction: 2 PDL (Pays de Loire) not 2 PDF.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 216th and 217th JN.1 sequences both from Ontario, Canada. 4th and 5th from Ontario. 6th and 7th from Canada.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 218th JN.1 sequence. Also Ontario, Canada. 6th from Ontario. 8th from Canada.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 219th and 220th JN.1 sequences. Both from Denmark. 9th and 10th from Denmark.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 221st and 222nd JN.1 sequences. Both from England. 15th and 16th from England. 17th and 18th from the UK.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 223rd JN.1 sequence. 4th from Israel.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 3 more JN.1 sequences. 1 from Vienna, Austria. 1st from Vienna, 1st from Austria. 2 from Ontario, Canada. 7th and 8th from Ontario, 9th and 10th from Canada.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani Global total now 226 JN.1 sequences.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 227th JN.1 sequence. Stockholm, Sweden. 1st from Stockholm, 1st from Sweden.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 228th JN.1 sequence. Galicia, Spain. 1st from Galicia, 9th from Spain.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 229th and 230th JN.1 sequences. 17th and 18th from England. 19th and 20th from the UK.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 231st and 232nd JN.1 sequences. Berlin and Baden-Wurttemberg, Germany. 1st from Berlin, 1st from Baden-Wurttemberg, 3rd and 4th from Germany.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 233rd JN.1 sequence. Newfoundland and Labrador, Canada. 1st from Newfoundland and Labrador, 11th from Canada.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 7 more JN.1 sequences. 2 from Denmark (11th and 12th from Denmark); 1 from Vorarlberg, Austria (1st from Vorarlberg, 2nd from Austria); 2 from Slask, Poland (1st 2 from Slask and from Poland); 2 from Basque Country, Spain (1st 2 from Basque Country, 10th and 11th Spain).

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani Global known JN.1 sequences now 240.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 241st JN.1 sequence. 19th from England. 21st from the UK.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 242nd JN.1 sequence. 1st from Taiwan.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 243rd JN.1 sequence. 1st from Canary Islands.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 7 more JN.1 sequences. 1 from Varna, Bulgaria (1st from Varna, 2nd from Bulgaria.) 1st 6 from Finland. Global known JN.1 sequence total now 250.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 251st JN.1 sequence. Bern, Switzerland. 1st from Bern, 7th from Switzerland.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 252nd JN.1 sequence. Counties Manukau, New Zealand. 1st in Counties Manukau, 1st in New Zealand.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 39 new JN.1 sequences. 2 NSW, Australia (1st 2 NSW and Australia). 1 Wales (2nd Wales, 22nd UK). 36 France h/t @siamosolocani (new JN.1 by region 3 BRE, 6 CVL, 3 GES, 16 IDF, 2 NOR). France total known JN.1 sequences now 126. Global total known JN.1 sequences now 291.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 292nd JN.1 sequence. Viken, Norway. 1st in Viken, 1st in Norway.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 5 new JN.1 sequences from Netherlands. 1st 2 from Noord-Brabant, 1st from Noord-Holland, 1st from Gelderland, 1st from Groningen. Netherlands known JN.1 sequence total 11. Global known JN.1 sequence total 297.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 298th JN.1 sequence. Catalunya, Spain. 1st from Catalunya, 12th from Spain.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 12 new JN.1 sequences. 8 more from Denmark (Denmark total 20). 4 more from Umbria, Italy (Umbria total 5, Italy total 7). Global total known JN.1 sequences 310.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 2 more JN.1 sequences. Shanghai, China. 1st 2 in Shanghai, 1st 2 in PRC China.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani Global known JN.1 sequences 312.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 313th JN.1 sequence. Walloon Brabant, Belgium. 6th from Belgium.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 5 new JN.1 sequences. 1 Skane, Sweden (1st Skane, 2nd Sweden), and 4 Hyogo, Japan (1 at 4 from Hyogo, 2nd to 5th from Japan.) Global total known JN.1 sequences now 318.

@LongDesertTrain @RajlabN @HNimanFC @JosetteSchoenma @siamosolocani 12 more JN.1 sequences. 1 from Croatia. (1st from Croatia). 11 from England. (England total 30, UK total 33.) Global total known JN.1 sequences 330.