The Analytic Garden

Vietnam has uncovered a new COVID-19 variant combining characteristics of the two existing variants first found in India and the UK, ~ Vietnam Health Minister Nguyen Thanh Long  This is the one that actually gets me concerned, Dr. Daniel Griffin, chief of infectious diseases for ProHEALTH, told CNBC, referring to the E484K mutation. It seems like every news cycle brings stories of a new SARS-CoV-2 variant. Even though in the US cases are dropping, the world is far from putting COVID-19 behind it. The US one-dose vaccination level is about 50% at the end of May 2021. Unfortunately, much of the world is far below this level . As long as there are vulnerable populations new variants will arise.  The B..617.3 variant has been in the news lately. Pango-Lineages lists three lineages with assigned sequences in the B.1.617 family: B.1.617.1, B.1.617.2, B.1.617.3. B.1.617.1 is the original variant in this group. I'll use the code from here  and here  to take a quick look a...

As viral sequencing ramps up, more variants will be detected. Currently, three variants appear to be of concern: B.1.1.7, B.1.351, and P.1, first detected in the UK, South Africa, and Brazil, respectively. B.1.1.7 has an unusually large number of mutations, including many in the spike protein. Although this is the best established for B.1.1.7, all of these variants may transmit better from person to person. (Posted January 19, 2021)  - Kartik Chandran, PhD  Professor of Microbiology and Immunology, Albert Einstein College of Medicine So far, one mutation, D614G, that occurred early last year quickly became the predominant strain worldwide. It allows the virus to replicate more efficiently in the upper airway to enhance shedding and the efficiency of transmission. Fortunately, this substitution does not render the virus resistant to the antibodies generated in vaccinated persons. Likewise, another substitution in the spike, N501Y, which is shared by both the UK and S. African v...

Be fast, have no regrets... If you need to be right before you move, you will never win, ~ Mike Ryan, epidemiologist at WHO, in March This is evolving science. You are seeing sausages being made — in front of the world’s eyes, ~ Yale vaccine researcher Saad Omer The SARS-CoV-2 virus keeps evolving and the number of genome sequences deposited in various repositories keeps growing. The NCBI Virus database currently has 193,819 sequences. On May 5, 2021 I downloaded the GISAID metafile. It has 1,355,996 records. The plot below shows the counts of sequence records at GISAID for each day vs. collection date. You can see the growth in sequence data in 2021. I wanted to look at the growth in the USA of three variants of interest: B.1.1.7 , called the United Kingdom variant; B.1.352, the South African variant; and P.1 the Brazil variant. Giving these variants country names doesn't necessarily mean that they developed in those countries. Rather, they have been extensively reported in thos...