Two UK Variant COVID Sequences In San Paulo Brazil

[niman]

Instituto de Medicina Tropical de Sao Paulo has released (at GISAID), two UK Variant COVID sequences (Brazil/SP-L67-CD1713/2020 & Brazil/SP-L67-CD1714/2020) from Dec 22 and 21 collections.

Edited January 1, 2021 by niman
Spike deletion present inn submitted sequences

[niman]

Brazil/SP-L67-CD1713/2020 12/22 24F matched UK variant with 3 AAs deleted in Spike protein, 3 AAs deleted in NSP6 and Q27 stop codon in NS8.

map update

https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=-23.526058698893912%2C-49.32148665163512&z=6

Edited January 1, 2021 by niman
Spike deletions present

[niman]

Brazil/SP-L67-CD1713/2020 12/21 34M matched UK variant with 3 AAs deleted in Spike protein, 3 AAs deleted in NSP6 and Q27 stop codon in NS8.

map update

https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=-23.526058698893912%2C-49.32148665163512&z=6

Edited January 1, 2021 by niman
Spike deletion present in submitted sequences

[niman]

DECEMBER 31, 20201:13 PMUPDATED AN HOUR AGO

Brazil detects two cases of new coronavirus variant found in UK

By Reuters Staff

 

A Brazilian lab said on Thursday it has detected two cases of the new coronavirus variant that has spread rapidly in Britain, and urged reinforcement of quarantine measures for travelers coming from Europe.

Diagnostic medicine company Dasa said in a statement that it had detected the SARS-CoV-2 strain B.1.1.7 through genetic sequencing done in partnership with Sao Paulo University’s Tropical Medicine Institute.

“Sequencing confirmed that the new strain of the virus has arrived in Brazil,” said researcher Ester Sabino at the Tropical Medicine Institute.

The new variant has rapidly become the dominant strain in cases of COVID-19 in parts of southern England, and has been linked to an increase in hospitalization rates. Australia, Italy and the Netherlands say they detected cases of the new strain.

https://in.reuters.com/article/us-health-coronavirus-brazil-variant/brazil-detects-two-cases-of-new-coronavirus-variant-found-in-uk-idINKBN2951LL

[niman]

https://twitter.com/CaddeProject/status/1344714122429145090/photo/1

[niman]

We report the first two cases caused by the SARS-CoV-2 B.1.1.7 (also known as Variant of Concern 202012/01, VOC) lineage in Brazil. The findings come less than 36 hours upon sample collection. Samples were immediately analyzed using a portable DNA sequencer as part of genomic surveillance activities from the Brazil-UK CADDE project. Sequencing and phylogenetic analysis confirm two separate introductions of the VOC lineage in Brazil, possibly from the UK. One case reported no travel outside of Brazil. Given the higher transmissibility of the VOC compared to non-VOC lineages, increased genomic surveillance is urgently needed to investigate the extent of VOC circulation in the country.

https://www.caddecentre.org/?page_id=15

[niman]

DETAIL

https://www.dropbox.com/s/y99g4uw6s7za01c/CADDE genomic report 31 Dec 2020.pdf?dl=0

[niman]

 

Instituto de Medicina Tropical de Sao Paulo has released (at GISAID), two UK Variant COVID sequences (Brazil/SP-L67-CD1713/2020 & Brazil/SP-L67-CD1714/2020) sans Spike deletions from Dec 22 and 21 collections.

The above sequence had incomplete regions in the spike gene, which included the positions encoding positions 69/70.  These sequences do have the deletion and were detected as S drop outs (PCR test of Spike gene creates a false negative).