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”

 

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Brazil: First confirmed death from #coronavirus REINFECTION reported

A 39-year-old Brazilian man who died of COVID-19 last month was suffering from a second bout of the illness, researchers said on Tuesday, making it the country’s first confirmed death from coronavirus reinfection. Both episodes involved variants with the E484K mutation.

The man, from Campo Bom in the southern state of Rio Grande do Sul, had a history of chronic cardiovascular disease and diabetes. He first tested positive on November 30 but details about his symptoms – if any – are unclear. Genomic sequencing revealed the P.1 variant.

The patient fell ill a second time about 3 months later and tested positive on March 11, according to researchers at Feevale University. His initial symptoms were fatigue and respiratory distress, but his condition worsened and he was transferred to the ICU, where he was intubated and died on March 19.

Genomic sequencing of the sample from the second episode revealed the P.2 variant, which is classified as a Variant of Interest.

 

 

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India: New Indian #coronavirus variant B.1.618 with added E484K

E484K has been found in a new Sars-Cov-2 variant labelled as B.1.618, which has been reported in West Bengal, India.

Data submitted from India to the global repository GISAID shows the B.1.618, at 12%, is the third most common variant sequenced in the last 60 days. The B.1.617, at 28%, is the most common among sequences, followed by B.1.1.7 (the UK variant), the India Mutation Report by Scripps Research showed, citing the GISAID data

Hindustan Times report

 

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Brazil: novel #coronavirus variant VUI-NP13L reported along with 2 cases of coinfection with B.1.1.28

“We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484K) with either B.1.1.248 or B.1.91 lineages. Also, clustering analysis revealed the occurrence of a novel cluster of samples circulating in the state (named VUI-NP13L) characterized by 12 lineage-defining mutations.”

ScienceDirect.com preprint:  Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

 

 

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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

 

 

 

1,039 cases of Brazilian #coronavirus variant P.1 reported in Canada

health-infobase.canada.ca

 

 

Brazilian #coronavirus variant P.1 now second most common variant in USA

“For the first time, however, the P.1 variant that originated in Brazil has taken the No. 2 spot. At least 434 people in the United States have been infected with the variant, which has devastated Brazil, with the largest number of cases found in Massachusetts, Illinois and Florida.”

 

 

Washington Post report

Chart courtesy of CDC

 

 

Detection of 54 cases of the P.1 variant in Massachusetts in less than a month

All three global VoCs (B.1.1.7, B.1.351, and P.1) have now been detected in MA. However, unlike B.1.1.7 and B.1.351, P.1 has shown a rapid rise in frequency in the few weeks following its first detection on March 16th, 2021.  Phylogenetic analysis of these 54 P.1 genomes from MA, alongside four additional P.1 genomes from neighbouring states (two from Connecticut (CT) and one each from Maine (ME) and Rhode Island (RI)) and 895 other global P.1 sequences from GISAID, 6 1 suggests at least six introductions of P.1 into MA and at least eight introductions of P.1 into the New England region, likely from both international and domestic sources.

Virological.org preprint  – Detection of a large cluster and multiple introductions of the P.1 SARS-CoV-2 Variant of Concern in Massachusetts

 

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Identification of a new B.1.1.33 SARS-CoV-2 Variant of Interest (VOI) circulating in Brazil with mutation E484K and multiple deletions in the Spike protein

Here, we report a new SARS-CoV-2 VOI derived from lineage B.1.1.33, preliminary designated as PANGO lineage N.10, harboring 14 lineage defining mutations. It displays as the most remarkable genetic changes the V445A and E484K mutations in the S protein RBD, several non-synonymous mutations (P9L, I210V, and L212I), and three deletions (∆141-144, ∆211, and ∆256-258) in the S protein NTD, including a truncated NS7b protein due to a frame-shifting deletion. Other five lineage-defining mutations were found among NSP3, NSP5, NSP6, and N. This VOI probably emerged in late December 2020 and comprises a significant fraction (23%) of the SARS-CoV-2 positive cases detected in the Brazilian state of Maranhão (Northeastern region), between January and February 2021.

Virilogical.org preprint

 

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Peru: 40% of #coronavirus cases in Lima are caused by the P.1 Brazilian variant

Approximately 40% of cases of the new coronavirus in Lima have been due to the P.1 Brazilian variant of this disease, according to a study carried out by the Peruvian National Institute of Health (INS).

This was indicated in a press conference by the Minister of Health, Óscar Ugarte . He added that the advance of this variant that has already passed through Loreto and Huánuco is being determined .

“This INS study is extremely important because it has made it possible to identify, through a sampling throughout Lima, that the main variant that causes COVID-19 today in a percentage of 40% is the Brazilian variant,” he said.

RPP.pe report

 

 

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USA: 50 cases of #coronavirus variant P.1 found in Barnstaple County, Cape Cod

Genetic sequencing of positive COVID-19 cases in the past week in Barnstable County, Cape Cod, has resulted in the identification of 50 cases of the P.1 virus variant that originated in Brazil, according to the state Department of Public Health. That’s all but seven of the 57 cases of P.1 that have been detected statewide, the DPH said. The state’s first case, announced March 16, was a Barnstable County woman in her 30s.

Cape Cod Times report

 

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Canada: #coronavirus variant P.1 outbreak spreads to Alberta

“We are currently investigating a significant #COVID19AB outbreak in Alberta involving P.1 variants of concern (the variant that originated in Brazil), linked to a returning traveller.”

 

 

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Denmark: 2 cases of B.1.1.7 #coronavirus variant found with E484K mutation

Denmark has found the first two cases of the UK coronavirus variant B.1.1.7, which has been mutated to have reduced sensitivity to antibodies, says Minister of Health Magnus Heunicke (S).

The variant is immediately the same as the one commonly referred to as B117 – the British variant of coronavirus – but it has the mutation E484K.

According to the Statens Serum Institut (SSI), the E484K mutation has so far only been seen in the B117 variant in the UK and the Netherlands.

Berlingske.dk report

 

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