sars-cov-2 genbank failed genbank deposit

 

https://www.science.org/content/article/first-sars-cov-2-genome-deposited-us-database-earlier-than-previously-known

this news discussed the need to pathogenic potential

 

Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland

Author links open overlay panel, , , , , , , , , , , , , , , , , , , …

https://www.sciencedirect.com/science/article/pii/S1755436521000335?via%3Dihub

2.2. Statistical inference

We fit a logistic model to the frequency of B.1.1.7 samples per day to estimate the logistic growth rate a and the sigmoid’s midpoint t0. From that, we derive an estimate of the transmission fitness advantage of B.1.1.7 under a continuous (fc) and a discrete (fd) model. Each model could plausibly describe the actual dynamics, so we present results from both for comparison. Further, we estimate the reproductive number R for the B.1.1.7 and non-B.1.1.7 infections. The mathematical derivations are described in the supplementary materials in the sections A.3 and A.4. Finally, we show the projected number of confirmed infections in the future under the continuous model. We initialize the model on 01 January 2021 with the estimated number of B.1.1.7 and non-B.1.1.7 confirmed infections on that day. We assume a reproductive number for the non-B.1.1.7 infections as estimated on the national level for 01 January-17 January 2021. Further, we assume that the expected generation time is 4.8 days and the fitness advantage is the estimated fc for the region and dataset of interest (Table 1).

P132H Mpro

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8923085/pdf/41422_2022_Article_640.pdf

SARS-CoV-2: wastewater surveillance sample from wastewater metagenome

https://www.ncbi.nlm.nih.gov/biosample/?term=wastewater+surveillance+sample+sars-cov-2 

 SARS-CoV-2: wastewater surveillance sample from wastewater metagenome

https://www.ncbi.nlm.nih.gov/biosample/?term=wastewater+surveillance+sample+sars-cov-2+Tennessee

Freyja

 Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.

https://github.com/andersen-lab/Freyja

GISAID and NCBI sars-cov-2 reference genomes

NCBI uses wuhan-hu-1

GISAID uses wuhan-hu-4. 

The two sequences only differ in the polyA tails. Qin verified this using MEGA alignment. 

So, wuhan-hu-1 and wuhan-hu-4 share the same gene coordinates, same GFF 

GISAID Wuhan reference strain

 

hCoV-19/Wuhan/WIV04/2019|EPI_ISL_402124|2019-12-30|China
48740

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

 

sars-cov-2 nextstrain phylogeny

 

Omicron is from an 'ancient' branch, different from Delta. It seems that phylogenetic success is not a good measure to compare Delta and Omicron fitness.