predicting new viral variants

 

Flagship unwraps new AI biotech that looks to predict variants before they’re here

https://endpts.com/flagship-unwraps-new-ai-biotech-that-looks-to-predict-variants-before-theyre-here/

Pando lineage

LB notes: 

 

Here is a link to a quick program that shows all of the pango lineages in GRA submissions for the updated GISAID variant surveillance dataset. There are 199 unique pango lineages out of all GRA submissions.

 

https://github.com/QinLab/LB-clade-fitness/blob/main/GRA_lineages.ipynb

 

Also, here are a couple links that might explain some of the unexpected ones:

 

https://virological.org/t/pango-lineage-nomenclature-provisional-rules-for-naming-recombinant-lineages/657

 

https://www.who.int/activities/tracking-SARS-CoV-2-variants

 

COVID variants B.1.1.529 Omicron

betacoronavirus

GR

B.1.1.529

2021-11-18

(NSP5_P132H,Spike_H69del,Spike_T95I,Spike_A67V,Spike_S373P,Spike_Q493R,Spike_H655Y,N_R203K,Spike_N969K,Spike_N856K,Spike_G142D,NSP3_A1892T,Spike_Q954H,N_P13L,NSP3_L1266I,Spike_N501Y,N_R32del,M_Q19E,Spike_N440K,NSP4_T492I,NSP6_L105del,Spike_N679K,Spike_N764K,Spike_L212I,Spike_Y505H,NSP6_G107del,NSP6_I189V,Spike_T547K,M_D3G,Spike_D796Y,N_G204R,Spike_T478K,Spike_V143del,M_A63T,Spike_G496S,NSP3_V1069I,Spike_K417N,NSP6_S106del,Spike_S371L,Spike_G339D,NSP3_S1265del,NSP14_I42V,Spike_P681H,Spike_Y144del,Spike_ins214EPE,N_S33del,Spike_S375F,Spike_Q498R,Spike_G446S,Spike_S477N,N_E31del,NSP3_K38R,Spike_N211del,Spike_E484A,E_T9I,Spike_V70del,Spike_L981F,NSP12_P323L,Spike_D614G,Spike_Y145del)

VOC Omicron GR/484A (B.1.1.529) first detected in Botswana/Hong Kong/South Africa

2021-11-11

Africa / Botswana / South East / Greater Gaborone / Gaborone

Human

2021-11-23

TRUE

0.0131383910524

0.379838874855

29684

 

B1.1.529 immuno comprosied person of origin

 

https://english.alarabiya.net/coronavirus/2021/11/26/Explainer-What-is-the-new-B-1-1-529-COVID-19-variant-

COVID19 B1.1.7 strain Alpha variant

 

https://en.wikipedia.org/wiki/SARS-CoV-2_Alpha_variant

https://theconversation.com/why-new-covid-19-variants-are-on-the-rise-and-spreading-around-the-world-153530?utm_medium=ampfacebook&utm_source=facebook&fbclid=IwAR2gt4EmnEcDFq3kGCZ-JHYJ3GGwPC9L5gr8ga6z82BZLg1lBlJs5lPk4Qo

Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data

Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England
https://virological.org/t/transmission-of-sars-cov-2-lineage-b-1-1-7-in-england-insights-from-linking-epidemiological-and-genetic-data/576

https://www.medrxiv.org/content/10.1101/2020.12.24.20248822v1

One study showed that N501Y had only a weak transmission advantage on its own, rising rapidly only when coupled with the suite of mutations observed in B.1.1.7.

Early empirical assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020
https://www.medrxiv.org/content/10.1101/2020.12.20.20248581v2