From 9992e98c8c69e81c3e7e2f81fd44713f17de9900 Mon Sep 17 00:00:00 2001 From: Memorable Date: Mon, 11 Sep 2023 22:34:31 +0800 Subject: [PATCH 1/4] Update lineage_notes.txt --- lineage_notes.txt | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 3c34430b..4090aaf0 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -2907,7 +2907,7 @@ FL.4.7 Alias of XBB.1.9.1.4.7, S:L452R, Singapore, from sars-cov-2-variants/line FL.4.8 Alias of XBB.1.9.1.4.8, S:478R, Indonesia, from #2024 FL.4.9 Alias of XBB.1.9.1.4.9, S:S254P, ORF3a:D173G, from #2081 FL.4.10 Alias of XBB.1.9.1.4.10, S:V1129I, China, from #2087 -FL.4.11 Alias of XBB.1.9.1.4.11, S:D1259Y, N:T334I, China/Japan +FL.4.11 Alias of XBB.1.9.1.4.11, S:D1259Y, N:T334I, China/Japan，from #2074 FL.5 Alias of XBB.1.9.1.5, N:T362I FL.5.1 Alias of XBB.1.9.1.5.1, S:M177T, from #2041 FL.6 Alias of XBB.1.9.1.6, ORF1a:I849V, Bahrain/Egypt/Oman/Austria @@ -2981,7 +2981,7 @@ HK.1 Alias of XBB.1.9.2.5.1.1.1, S:G257V, China from https://github.com/sars-cov HK.2 Alias of XBB.1.9.2.5.1.1.2, S:Q14H, China From sars-cov-2-variants/lineage-proposals#432 HK.3 Alias of XBB.1.9.2.5.1.1.3, S:L455F, China from https://github.com/sars-cov-2-variants/lineage-proposals/issues/414 HK.3.1 Alias of XBB.1.9.2.5.1.1.3.1, S:F157L, China, from #2193 -HK.3.2 Alias of XBB.1.9.2.5.1.1.3.2, S:Q14K, China +HK.3.2 Alias of XBB.1.9.2.5.1.1.3.2, S:Q14K, China，from https://github.com/sars-cov-2-variants/lineage-proposals#730 HK.3.3 Alias of XBB.1.9.2.5.1.1.3.3, S:S256L, N:P364L, China/Singapore HK.4 Alias of XBB.1.9.2.5.1.1.4, S:T883I, China HK.5 Alias of XBB.1.9.2.5.1.1.5, S:Q677H, China @@ -3202,7 +3202,7 @@ XBB.1.46 ORF1a:C1114F, Singapore/Malaysia XBB.1.47 ORF1a:T1761I, ORF1a:C2180Y, ORF1a:I2854V, Philippines/Singapore/Japan XBB.1.47.1 S:486P, S:A260V, S:V1122G, Japan/USA/Australia/Germany XBB.1.48 S:L455F, S:F456L (22928C), C2509T, Pakistan, from #1681 -XBB.1.49 S:346S, S:486P, on C16648A, A27965G, pre ORF8:8* branch with XBB.1.33, Somalia from sars-cov-2-variants/lineage-proposals#208 +XBB.1.49 S:346S, S:486P, on C16648A, A27965G, pre ORF8:8* branch with XBB.1.33, Somalia from sars-cov-2-variants/lineage-proposals/#208 XBB.2 Defined by S:D253G, from issue #1173 XBB.2.1 Defined by S:N764R (C23853G), two step mutation on top of C23854A (S:N764K defining of all Omicrons) XBB.2.2 Defined by S:Q613H @@ -3214,14 +3214,14 @@ HH.1.1 Alias of XBB.2.3.2.1.1, S:G181A from sars-cov-2-variants/lineage-proposa HH.2 Alias of XBB.2.3.2.2, ORF1a:D48Y XBB.2.3.3 S:182N, India/USA From #1810 GJ.1 Alias of XBB.2.3.3.1, found mainly in China and USA, from pango-designation issue #2005 -GJ.1.1 Alias of XBB.2.3.3.1.1, S:A222V, N:R319H, ORF1a:V1915I From sars-cov-2-variants/lineage-proposals#109 +GJ.1.1 Alias of XBB.2.3.3.1.1, S:A222V, N:R319H, ORF1a:V1915I From sars-cov-2-variants/lineage-proposals/109 GJ.1.2 Alias of XBB.2.3.3.1.2, ORF1b:V1110I, from #2059 -GJ.1.2.1 Alias of XBB.2.3.3.1.2.1, S:N450D, Singapore/Thailand/South Korea/USA/Spain From sars-cov-2-variants/lineage-proposals#446 -JE.1 Alias of XBB.2.3.3.1.2.1.1, S:478R, Singapore/SouthKorea/US From sars-cov-2-variants/lineage-proposals#597 +GJ.1.2.1 Alias of XBB.2.3.3.1.2.1, S:N450D, Singapore/Thailand/South Korea/USA/Spain From sars-cov-2-variants/lineage-proposals/446 +JE.1 Alias of XBB.2.3.3.1.2.1.1, S:478R, Singapore/SouthKorea/US From sars-cov-2-variants/lineage-proposals/597 GJ.1.2.2 Alias of XBB.2.3.3.1.2.2, S:478R, Europe/US/Australia GJ.1.2.3 Alias of XBB.2.3.3.1.2.3, S:T76I, Japan GJ.1.2.4 Alias of XBB.2.3.3.1.2.4, S:S255F, on ORF1a:H919Y branch, Japan/USA/South Korea -GJ.1.2.5 Alias of XBB.2.3.3.1.2.5, S:I834V, Singapore/South Korea/USA +GJ.1.2.5 Alias of XBB.2.3.3.1.2.5, S:I834V, Singapore/South Korea/USA，from https://github.com/sars-cov-2-variants/lineage-proposals/issues/628 GJ.2 Alias of XBB.2.3.3.2, S:I1114S, Europe GJ.3 Alias of XBB.2.3.3.3, ORF1a:P971S, ORF1b:V2371L GJ.4 Alias of XBB.2.3.3.4, S:M153I，from #1902 From bed44d0c4da93b01fa6cc7ad749c87f85e6d16b9 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sun, 24 Sep 2023 18:27:00 +0200 Subject: [PATCH 2/4] Update lineage_notes.txt --- lineage_notes.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 4090aaf0..1747e702 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -3202,7 +3202,7 @@ XBB.1.46 ORF1a:C1114F, Singapore/Malaysia XBB.1.47 ORF1a:T1761I, ORF1a:C2180Y, ORF1a:I2854V, Philippines/Singapore/Japan XBB.1.47.1 S:486P, S:A260V, S:V1122G, Japan/USA/Australia/Germany XBB.1.48 S:L455F, S:F456L (22928C), C2509T, Pakistan, from #1681 -XBB.1.49 S:346S, S:486P, on C16648A, A27965G, pre ORF8:8* branch with XBB.1.33, Somalia from sars-cov-2-variants/lineage-proposals/#208 +XBB.1.49 S:346S, S:486P, on C16648A, A27965G, pre ORF8:8* branch with XBB.1.33, Somalia from sars-cov-2-variants/lineage-proposals#208 XBB.2 Defined by S:D253G, from issue #1173 XBB.2.1 Defined by S:N764R (C23853G), two step mutation on top of C23854A (S:N764K defining of all Omicrons) XBB.2.2 Defined by S:Q613H From 18dead4b01fb14600658573de1856e2bc212b750 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sun, 24 Sep 2023 18:28:12 +0200 Subject: [PATCH 3/4] Apply suggestions from code review --- lineage_notes.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 1747e702..1890428d 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -3214,10 +3214,10 @@ HH.1.1 Alias of XBB.2.3.2.1.1, S:G181A from sars-cov-2-variants/lineage-proposa HH.2 Alias of XBB.2.3.2.2, ORF1a:D48Y XBB.2.3.3 S:182N, India/USA From #1810 GJ.1 Alias of XBB.2.3.3.1, found mainly in China and USA, from pango-designation issue #2005 -GJ.1.1 Alias of XBB.2.3.3.1.1, S:A222V, N:R319H, ORF1a:V1915I From sars-cov-2-variants/lineage-proposals/109 +GJ.1.1 Alias of XBB.2.3.3.1.1, S:A222V, N:R319H, ORF1a:V1915I From sars-cov-2-variants/lineage-proposals#109 GJ.1.2 Alias of XBB.2.3.3.1.2, ORF1b:V1110I, from #2059 GJ.1.2.1 Alias of XBB.2.3.3.1.2.1, S:N450D, Singapore/Thailand/South Korea/USA/Spain From sars-cov-2-variants/lineage-proposals/446 -JE.1 Alias of XBB.2.3.3.1.2.1.1, S:478R, Singapore/SouthKorea/US From sars-cov-2-variants/lineage-proposals/597 +JE.1 Alias of XBB.2.3.3.1.2.1.1, S:478R, Singapore/SouthKorea/US From sars-cov-2-variants/lineage-proposals#597 GJ.1.2.2 Alias of XBB.2.3.3.1.2.2, S:478R, Europe/US/Australia GJ.1.2.3 Alias of XBB.2.3.3.1.2.3, S:T76I, Japan GJ.1.2.4 Alias of XBB.2.3.3.1.2.4, S:S255F, on ORF1a:H919Y branch, Japan/USA/South Korea From 87a311372dbc40fea5880269bd6eae0a42c47145 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sun, 24 Sep 2023 18:29:20 +0200 Subject: [PATCH 4/4] Apply suggestions from code review --- lineage_notes.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 1890428d..81a12ab9 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -2981,7 +2981,7 @@ HK.1 Alias of XBB.1.9.2.5.1.1.1, S:G257V, China from https://github.com/sars-cov HK.2 Alias of XBB.1.9.2.5.1.1.2, S:Q14H, China From sars-cov-2-variants/lineage-proposals#432 HK.3 Alias of XBB.1.9.2.5.1.1.3, S:L455F, China from https://github.com/sars-cov-2-variants/lineage-proposals/issues/414 HK.3.1 Alias of XBB.1.9.2.5.1.1.3.1, S:F157L, China, from #2193 -HK.3.2 Alias of XBB.1.9.2.5.1.1.3.2, S:Q14K, China，from https://github.com/sars-cov-2-variants/lineage-proposals#730 +HK.3.2 Alias of XBB.1.9.2.5.1.1.3.2, S:Q14K, China，from sars-cov-2-variants/lineage-proposals#730 HK.3.3 Alias of XBB.1.9.2.5.1.1.3.3, S:S256L, N:P364L, China/Singapore HK.4 Alias of XBB.1.9.2.5.1.1.4, S:T883I, China HK.5 Alias of XBB.1.9.2.5.1.1.5, S:Q677H, China @@ -3216,7 +3216,7 @@ XBB.2.3.3 S:182N, India/USA From #1810 GJ.1 Alias of XBB.2.3.3.1, found mainly in China and USA, from pango-designation issue #2005 GJ.1.1 Alias of XBB.2.3.3.1.1, S:A222V, N:R319H, ORF1a:V1915I From sars-cov-2-variants/lineage-proposals#109 GJ.1.2 Alias of XBB.2.3.3.1.2, ORF1b:V1110I, from #2059 -GJ.1.2.1 Alias of XBB.2.3.3.1.2.1, S:N450D, Singapore/Thailand/South Korea/USA/Spain From sars-cov-2-variants/lineage-proposals/446 +GJ.1.2.1 Alias of XBB.2.3.3.1.2.1, S:N450D, Singapore/Thailand/South Korea/USA/Spain From sars-cov-2-variants/lineage-proposals#446 JE.1 Alias of XBB.2.3.3.1.2.1.1, S:478R, Singapore/SouthKorea/US From sars-cov-2-variants/lineage-proposals#597 GJ.1.2.2 Alias of XBB.2.3.3.1.2.2, S:478R, Europe/US/Australia GJ.1.2.3 Alias of XBB.2.3.3.1.2.3, S:T76I, Japan