From 4256d9b4f62f1fb14bfaf2240bd9aecd33e23cc6 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 18 Dec 2024 22:29:52 +0100 Subject: [PATCH] Designate NU.1 (JN.1.55.2 + S:R346T, S:Q677H, ORF3a:L52F, Brazil) and XEC.16 (S:T678I) --- lineage_notes.txt | 2 + lineages.csv | 111 ++++++++++++++++++++++++++++++- pango_designation/alias_key.json | 1 + 3 files changed, 113 insertions(+), 1 deletion(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 7cf7e99f..35624e97 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1575,6 +1575,7 @@ JN.1.54.1 Alias of B.1.1.529.2.86.1.1.54.1, S:F456L, S:V407I, Spain, from #2584 JN.1.55 Alias of B.1.1.529.2.86.1.1.55, ORF1a:K399R JN.1.55.1 Alias of B.1.1.529.2.86.1.1.55.1, S:F456L, ORF1a:T1017I, Thailand, from sars-cov-2-variants/lineage-proposals#1253 JN.1.55.2 Alias of B.1.1.529.2.86.1.1.55.2, S:F456L, ORF1b:P2321H, Brazil, from sars-cov-2-variants/lineage-proposals#1253 +NU.1 Alias of B.1.1.529.2.86.1.1.55.2, S:R346T, S:Q677H, ORF3a:L52F, Brazil JN.1.56 Alias of B.1.1.529.2.86.1.1.56, Orf3a:Q213K JN.1.56.1 Alias of B.1.1.529.2.86.1.1.56.1, S:G181R, S:R346T, S:F456V, ORF1a:T1638I, Sinapore/South Korea from #2582 JN.1.57 Alias of B.1.1.529.2.86.1.1.57, ORF1b:A1219S, A11947G @@ -4434,6 +4435,7 @@ XEC.12 S:G252S, T25039C XEC.13 S:S98F XEC.14 ORF1a:A138T XEC.15 ORF1b:M2322I, C9803T +XEC.16 S:T678I XED Recombinant lineage of JN.1.4 and LF.1.1.1 (breakpoint 19210-21652), from #2691 XEE Recombinant lineage of KP.2.3.7 and JN.1* (breakpoint 24873-25592), from #2721 XEF Recombinant lineage of LB.1.4 and KP.3 (breakpoint 22600-23038), from sars-cov-2-variants/lineage-proposals#1855 diff --git a/lineages.csv b/lineages.csv index 3c40af5c..4d167535 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2552468,7 +2552468,6 @@ Thailand/NIC_BKK_1005/2024,JN.1.55.1 Australia/WA16038/2024,JN.1.55.2 France/OCC-ChuMtp-99240351464/2024,JN.1.55.2 Australia/TAS007174/2024,JN.1.55.2 -USA/CA-GBW-GKISBBBB20761/2024,JN.1.55.2 France/HDF-IPP04622/2024,JN.1.55.2 France/ARA-HCL024035092501/2024,JN.1.55.2 Australia/SA1371183/2024,JN.1.55.2 @@ -2589927,3 +2589926,113 @@ Thailand/NIC_BKK_1950/2024,XER USA/CA-LACPHL-AY08962/2024,XER USA/CA-LACPHL-AY09142/2024,XER USA/CA-LACPHL-AY09127/2024,XER +Sweden/01_SE100_24CS101031/2024,XEC.16 +Sweden/01_SE100_24CS101052/2024,XEC.16 +Sweden/AB-01_SE100_24CS502571/2024,XEC.16 +Sweden/AB-01_SE100_24CS502589/2024,XEC.16 +Spain/AS-HUCA-232478125/2024,XEC.16 +Canada/BC-BCCDC-752665/2024,XEC.16 +Canada/BC-BCCDC-747485/2024,XEC.16 +Japan/FR050-0384/2024,XEC.16 +Japan/FR007-0100/2024,XEC.16 +Canada/AB-ABPHL-128282/2024,XEC.16 +Canada/AB-ABPHL-128118/2024,XEC.16 +Canada/AB-ABPHL-128317/2024,XEC.16 +Canada/AB-ABPHL-128480/2024,XEC.16 +Canada/AB-ABPHL-128426/2024,XEC.16 +Brazil/PE-FIOCRUZ-IAM17181/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM17193/2024,NU.1 +Italy/VEN-AOUIVR-7410731101_VR/2024,NU.1 +France/ARA-RELAB-HCL724000180801/2024,NU.1 +Brazil/RJ-FIOCRUZ-11284/2024,NU.1 +Brazil/SP-IB_CEVC_2400939/2024,NU.1 +Netherlands/FL-RIVM-139763/2024,NU.1 +USA/VA-GBW-GKPLAAAA31512/2024,NU.1 +USA/VA-GBW-GKISBBBD60369/2024,NU.1 +Brazil/SP-IAL-357884895/2024,NU.1 +Brazil/GO-FIOCRUZ-9599/2024,NU.1 +Brazil/MG-FUNED-312184831/2024,NU.1 +Italy/VEN-IZSVe-24RS8039-16_PD/2024,NU.1 +Italy/VEN-IZSVe-24RS8039-17_PD/2024,NU.1 +Brazil/ES-LACENES-321613818/2024,NU.1 +Brazil/ES-LACENES-321590890/2024,NU.1 +Brazil/GO-FIOCRUZ-8138/2024,NU.1 +USA/CA-GBW-GKISBBBB20761/2024,NU.1 +Spain/AN-PMC-40504/2024,NU.1 +Spain/AN-PMC-40498/2024,NU.1 +Spain/ML-HCM-01620121/2024,NU.1 +Spain/AN-PMC-41118/2024,NU.1 +Spain/AN-PMC-40497/2024,NU.1 +Brazil/AL-IB_CEVC_2400997/2024,NU.1 +Brazil/AL-IB_CEVC_2401010/2024,NU.1 +Brazil/AL-IB_CEVC_2401009/2024,NU.1 +Brazil/PB-036916-IEC/2024,NU.1 +Brazil/AL-IB_CEVC_2401019/2024,NU.1 +Brazil/AL-IB_CEVC_2400928/2024,NU.1 +Brazil/AL-IB_CEVC_2401173/2024,NU.1 +Brazil/AL-IB_CEVC_2401016/2024,NU.1 +Brazil/AL-IB_CEVC_2401003/2024,NU.1 +Brazil/AL-IB_CEVC_2401005/2024,NU.1 +Brazil/AL-IB_CEVC_2401008/2024,NU.1 +Brazil/RJ-FIOCRUZ-11286/2024,NU.1 +Brazil/AL-IB_CEVC_2401011/2024,NU.1 +Brazil/RJ-FIOCRUZ-10729/2024,NU.1 +Brazil/SE-FIOCRUZ-10069/2024,NU.1 +Brazil/BA-LACEN-293834598/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16791/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16801/2024,NU.1 +Brazil/PB-036955-IEC/2024,NU.1 +Brazil/PB-036959-IEC/2024,NU.1 +Brazil/PB-036995-IEC/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16701/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16811/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16787/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16789/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16819/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16795/2024,NU.1 +Brazil/ES-LACENES-321613783/2024,NU.1 +Italy/LOM-UNIBS-08059702/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16800/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16810/2024,NU.1 +Denmark/DCGC-687620/2024,NU.1 +Brazil/PB-036941-IEC/2024,NU.1 +Brazil/PB-036953-IEC/2024,NU.1 +Brazil/PB-036949-IEC/2024,NU.1 +Brazil/GO-LACENGO-520584711/2024,NU.1 +Brazil/BA-LACEN-293769729/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16711/2024,NU.1 +Brazil/PB-036931-IEC/2024,NU.1 +Brazil/PB-26217-IEC/2024,NU.1 +Brazil/ES-LACENES-321632254/2024,NU.1 +Brazil/ES-LACENES-321613807/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16799/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16798/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM17200/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16817/2024,NU.1 +Brazil/PB-036928-IEC/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16809/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM17186/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM17185/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM17191/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM17187/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM17178/2024,NU.1 +Brazil/AL-IB_CEVC_2401178/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16813/2024,NU.1 +Brazil/GO-FIOCRUZ-9627/2024,NU.1 +Brazil/GO-LACENGO-520584709/2024,NU.1 +Brazil/GO-LACENGO-520575978/2024,NU.1 +Brazil/GO-LACENGO-520575984/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16820/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16805/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16806/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM17220/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16797/2024,NU.1 +Brazil/PE-FIOCRUZ-IAM16815/2024,NU.1 +USA/CA-GBW-GKPLAAAA15362/2024,NU.1 +USA/CA-GBW-GKISBBBD40414/2024,NU.1 +USA/VA-GBW-GKISBBBC94588/2024,NU.1 +Brazil/PR-LACENPR-415744411/2024,NU.1 +Brazil/PR-FIOCRUZ-9695/2024,NU.1 +Brazil/PB-26218-IEC/2024,NU.1 +Brazil/PB-036940-IEC/2024,NU.1 +Brazil/MG-FUNED-312185105/2024,NU.1 diff --git a/pango_designation/alias_key.json b/pango_designation/alias_key.json index 192435c9..e4c31cd0 100644 --- a/pango_designation/alias_key.json +++ b/pango_designation/alias_key.json @@ -310,6 +310,7 @@ "NR": "B.1.1.529.2.86.1.1.11.1.3.1.11", "NS": "B.1.1.529.2.86.1.1.16.3", "NT": "B.1.1.529.2.86.1.1.16.1.7.1.2", + "NU": "B.1.1.529.2.86.1.1.55.2", "XA": ["B.1.1.7","B.1.177"], "XB": ["B.1.634","B.1.631"], "XC": ["AY.29","B.1.1.7"],