NEJM: In two #coronavirus vaccine breakthrough cases “examination of the SARS-CoV-2 sequences revealed that both patients were infected with variant viruses” .. “neither sequence precisely fit any known clade”

Examination of the SARS-CoV-2 sequences revealed that both patients were infected with variant viruses. Rapid identification of sequence variants by targeted PCR amplification showed that neither sequence precisely fit any known clade. Some of the substitutions in Patient 1 (T95I, del144, E484K, A570D, D614G, P681H, and D796H) were shared with B.1.526 (T95I, E484K, and D614G6), and three substitutions were shared with Patient 2 (in whom the variants T95I, G142V and del144, F220I, R190T, R237K, R246T, and D614G were detected).

NEJM article  “Vaccine Breakthrough Infections with SARS-CoV-2 Variants”

 

Image by Daniel Roberts from Pixabay

Africa: Tanzania/Angola #coronavirus variant carries E484K & H655Y mutations

Forbes are carrying an interesting about the recently discovered coronavirus variant found in Tanzania, Africa in travellers arriving from Angola.  The variant is from “From An Entirely New Branch Of SARS-CoV-2”, and carries Spike mutations E484K, P681H, T478R, Q957H, H655Y, D215G, D80Y. L210N, W258L, R246I.  “An additional 18 amino acid changes occur in proteins outside the spike protein. These include 14 in the orf1ab proteins that specify the replication complex. “

“This is a remarkable illustration of convergent evolution,” say’s Forbes

Forbes article: New Tanzanian Variant Detected In Angola From An Entirely New Branch Of SARS-CoV-2

 

 

 

New SARS-CoV-2 #coronavirus lineage that shares mutations with known Variants of Concern (VOC) reported in 20 states across USA

We report a SARS-CoV-2 lineage that shares N501Y, P681H, and other mutations with known variants of concern, such as B.1.1.7. This lineage, which we refer to as B.1.x (COG-UK sometimes references similar samples as B.1.324.1), is present in at least 20 states across the USA and in at least six countries. However, a large deletion causes the sequence to be automatically rejected from repositories, suggesting that the frequency of this new lineage is underestimated using public data.

Recent dynamics based on 339 samples obtained in Santa Cruz County, CA, USA suggest that B.1.x may be increasing in frequency at a rate similar to that of B.1.1.7 in Southern California. At present the functional differences between this variant B.1.x and other circulating SARS-CoV-2 variants are unknown, and further studies on secondary attack rates, viral loads, immune evasion and/or disease severity are needed to determine if it poses a public health concern.

BiorXiv preprint:   A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control

Image by Jürgen Jester from Pixabay