New #coronavirus variant in #Oregon has B.1.1.7 backbone with E484K mutation – “seems to have evolved independently”

The new coronavirus variant that surfaced in Oregon has the same B.1.1.7 backbone, but also a mutation – E484K, or “Eek” – seen in variants of the virus circulating in South Africa, Brazil and New York City.

Lab studies and clinical trials in South Africa indicate that the Eek mutation renders the current vaccines less effective by blunting the body’s immune response. The vaccines still work, but the findings are worrying enough that Pfizer-BioNTech and Moderna have begun testing new versions of their vaccines designed to defeat the variant found in South Africa.

The B117 variant with Eek also has emerged in Britain, designated as a “variant of concern” by scientists. But the virus identified in Oregon seems to have evolved independently, Prof O’Roak said. He and his colleagues found the variant among coronavirus samples collected by the Oregon State Public Health Lab across the state, including some from an outbreak in a health care setting.

Straits Times Report


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Imperial College: #SARSCoV2 #coronavirus variant #P1 is more transmissible, evasive, and growing rapidly in Brazil

Researchers estimate that the P.1 VOC is between 1.4–2.2 times more transmissible than non-VOC lineages. In addition, they estimate that the P.1 VOC evades 25-61% of protective immunity arising from infection with previously circulating variants.

Statistical analysis of genome data suggests that the P.1 lineage has likely been circulating in Manaus since early November 2020.

This lineage has been identified in over 20 countries worldwide and continues to spread, including several recently confirmed cases in the UK.

Global collaborative efforts on rapid virus genome sequencing are allowing us to identify SARS-CoV-2 lineages of concerns in near real-time.

Several genetic changes – substitutions and deletions – in this new P.1 lineage may have immunological significance. The team identified 17 mutations for this VOC, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor: a protein on the cell surface functioning as an entrance into the cell for SARS-CoV-2. Using analysis of genome sequence data, researchers were able to date back the emergence of the P.1 VOC to early November 2020.
More transmissible and evasive

The researchers found that the new P.1 lineage is growing rapidly in Brazil, is likely more transmissible than other variants, and may have the ability to evade protective immunity. The researchers estimate that the P.1 VOC is between 1.4–2.2 times more transmissible than non-VOC lineages. In addition, they estimate that the P.1 VOC evades 25-61% of protective immunity arising from infection with previously circulating variants. The exact trade-off between increased transmissibility and evading immunity is not currently known.

Imperial College report


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WHO: The #coronavirus pandemic has caused mass trauma on a larger scale than World War II

The Covid-19 pandemic has caused mass trauma on a larger scale than World War II, and the impact will last “for many years to come,” the World Health Organization’s top official said Friday.

“After the Second World War, the world has experienced mass trauma, because Second World War affected many, many lives. And now, even with this Covid pandemic, with bigger magnitude, more lives have been affected,” WHO Director-General Tedros Adhanom Ghebreyesus said at a news conference Friday. “Almost the whole world is affected, each and every individual on the surface of the world actually has been affected.”

“And that means mass trauma, which is beyond proportion, even bigger than what the world experienced after the Second World War,” he added, noting the effect on mental health. “And when there is mass trauma, it affects communities for many years to come.”

CNBC report

More #E484K #B1128 #coronavirus co-infections reported in #Brazil

B.1.1.28 (E484K) is able to establish successful coinfection events co-occurring simultaneously with different lineages of SARS-CoV-2.

The novel variant B.1.1.28 (E484K) previously described in Rio de Janeiro is currently spread across the southernmost state of Brazil.

The novel variant VUI-NP13L was also identified by causing a local outbreak in Rio Grande do Sul.

Medrxix paper  – 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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Orangutans at San Diego zoo receive first #coronavirus vaccine made for animals

“An orangutan named Karen, the first in the world to have open-heart surgery in 1994, has made medical history again: She’s among the first great apes to get a COVID-19 vaccine.

In February, Karen, three other orangutans, and five bonobos at the San Diego Zoo have received two doses each of an experimental vaccine for animals developed by a veterinary pharmaceutical company, says Nadine Lamberski, chief conservation and wildlife health officer at the San Diego Zoo Wildlife Alliance.”

Full National Geographic article


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Doctors report large skin rashes appeared in 12 patients in delayed reaction to Moderna mRNA-1273 #coronavirus vaccine

“We have also observed delayed large local reactions to the mRNA-1273 vaccine, with a median onset on day 8 (range, 4 to 11) after the first dose. These reactions had a variable appearance. Here, we report on a series of 12 patients with these reactions, all of which appeared near the injection site after complete resolution of the initial local and systemic symptoms associated with vaccination.”

New England Journal of Medicine report

16 cases of new #coronavirus variant VUI-202102/04, B1.1.318 under investigation in Britain

Sixteen cases of a new variant, VUI-202102/04 (lineage B.1.1.318), have been identified in the UK. The variant has been designated a Variant Under Investigation (VUI) by Public Health England (PHE).

Cases of this variant, understood to have originated in the UK, were first identified on 15 February through genomic horizon scanning. All individuals who tested positive and their contacts have been traced and advised to isolate.

Following assessments, the variant was designated a VUI on 24 February. It contains the E484K mutation, which is also found in 2 existing VUIs present in the UK, but does not feature the N501Y mutation, present in all variants of concern (VOCs).

The addition of this variant as a VUI means there are now a total of 4 VUIs and 4 VOCs currently being tracked in the UK. variant statement

Daily Mail report


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First case of the #P1 Brazil #coronavirus variant found in Denmark with mutations #501YV3, #N501Y, #K417T & #E484K

Denmark’s SSI:  The Technical University of Denmark, DTU, has found a case of the P1 variant, which was originally detected in Brazil.

The virus variant is also called VOC 202101/02 (Variant Of Concern, year 2021, month 01, variant 02). It has also been named 501Y.V3 after one of the key mutations. The Danish case has been found on Zealand.Mutations N501Y, K417T and E484K in particular are biologically important. As this variant has the mutation N501Y, which variants B.1.1.7 and B.1.351 also have, there is a strong suspicion that this variant has increased infectivity, but this has not been conclusively proven. This variant also has the mutation E484K, which studies have associated with decreased sensitivity to neutralizing antibodies. It is not known whether this variant causes more serious disease courses.

The variant was found by sequencing positive PCR samples performed by DTU’s Center for Diagnostics and the sample has just been completely sequenced, and thus confirmed.

The vaccines that are approved in the EU incl. Denmark, is also expected to work against the new variant. Impaired effects may occur, but the vaccines are still expected to protect against serious illness.

Denmark’s SSI report


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11 escaped #mink tested positive for #SARSCoV2 #coronavirus antibodies in Utah

“Serum samples from the 11 mink escapees tested positive for SARS-CoV-2 antibodies by virus neutralization”

We captured 102 mammals (78 rodents and 24 mesocarnivores). Rodent captures consisted of 45 deer mice (Peromyscus maniculatus), 5 Peromyscus spp. mice, 25 house mice (Mus musculus), and 3 rock squirrels (Otospermophilus variegatus). Mesocarnivore captures consisted of 11 presumed escaped American mink (Neovison vison), 2 presumed wild American mink, 5 raccoons (Procyon lotor), and 6 striped skunks (Mephitis mephitis). Presumed escaped mink were closely associated with barns and designated as domestic escapees on the basis of location, behavior, and appearance. We identified wild mink by brown coat color and smaller size compared with farmed mink. All escaped mink and rodents, except for 4 deer mice and 1 rock squirrel, were caught on farm premises. All raccoons, the 2 presumed wild mink, and all but 1 striped skunk were captured off-property but within the buffer zone.

Serum samples from the 11 mink escapees tested positive for SARS-CoV-2 antibodies by virus neutralization (Table). No other animal had a detectable antibody response. Of the antibody-positive escaped mink, 3 also had high cycle threshold (Ct) detections by rRT-PCR of nasal swabs (range Ct 35.89–38.95) and 1 lung tissue specimen (Ct 39.2 for N1). A rectal swab specimen from a house mouse had a high Ct detection by rRT-PCR but was negative for SARS-CoV-2 antibodies. N1 alone was detected by rRT-PCR in 2 samples from deer mice (Ct 37.55 and 39.57).


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Genomics and epidemiology of a novel #SARSCoV2 lineage in Manaus, Brazil #P1 #coronavirus

Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor.

Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4–2.2 times more transmissible and able to evade 25-61% of protective immunity elicited by previous infection with non-P.1 lineages.

Full Preprint Paper on Github (pdf file)


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Brazilian #coronavirus variant #P1 at 4.3% in Umbria, Tuscany, Lazio, and Marche in #Italy

“in our territory, in particular in some regions of central Italy ,there is an estimated prevalence of the Brazilian variant of 4.3%, not in the whole country, but in Umbria, Tuscany, Lazio, Marche”. This is “a particularly worrying fact. These variants are new and must be estimated both with respect to increased transmissibility and the potential not to guarantee the same immune coverage : increased transmissibility and the potential ability to reduce protection. They are extremely important to monitor and it is important that the most restrictive measures possible are taken.”  The variant South African , on the other hand, “is 0.4%  particularly in some areas of South Tyrol”.

The president of the CSS to reiterate that “the English variant has greater power infectious on the pediatric population . We have clear evidence. There is an increase in the number of cases even between 6 and 10 years “.

“The English variant has a greater transmission capacity. It has an estimated prevalence of around 54% , but it is a figure referred to February 18, so today the value is undoubtedly higher”.,

Comments by Silvio Brusaferro , president of the Italian ISS, and Franco Locatelli , President of the CSS. report


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Patients with #covid tied to stretchers in #Amazonas due to lack of sedatives

Patients with serious Covid-19 at the regional hospital in Parintins, Amazonas, are being tied with gauze onto their stretchers because of a lack of sedatives.

JN interviewed the president of the Brazilian Association of Intensive Care Medicine (AMIB), Suzana Lobo, who explained that the procedure is not wrong.  Lobo also said that intubating patients without sedation would be inhumane.

“[Without sedatives] The first thing that can happen is self-extubation, he [patient] removes the tube. This can lead to cardiac arrest (…) It is inhumane to imagine a person who will be kept on mechanical ventilation without be under analgesia and good sedation. She will feel discomfort, she will feel anxiety, she will feel fear … And all of this will lead to very serious consequences. ”