The mortality hazard ratio associated with infection with VOC-202012/1 [B.1.1.7] compared to infection with previously circulating variants is 1.64 in patients who have tested positive for COVID-19 in the community. In this comparatively low risk group, this represents an increase from 2.5 to 4.1 deaths per 1000 detected cases.
Medrxiv Preprint Increased hazard of mortality in cases compatible with SARS-CoV-2 variant of concern 202012/1 – a matched cohort study
Here, we describe the emergence of a new SARS-CoV-2 lineage, mainly from the Central Visayas region of the Philippines. This emergent variant is characterized by 13 lineage-defining mutations, including the co-occurrence of the E484K, N501Y, and P681H mutations at the spike protein region, as well as three additional radical amino acid replacements towards the C-terminal end of the said protein. A three-amino acid deletion at positions 141 to 143 (LGV141_143del) in the spike protein was likewise seen in a region preceding the 144Y deletion found in the B.1.1.7 variant. A single amino acid replacement, K2Q, at the N-terminus of ORF8 was also shared by all 33 samples sequenced.
Medrxiv paper Genome sequencing and analysis of an emergent SARS-CoV-2 variant characterized by multiple spike protein mutations detected from the Central Visayas Region of the Philippines
“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.”
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.
A new study has shown people previously infected by the Covid-19 variant 501Y.V2, originally identified in South Africa, have better immunity against other coronavirus mutations, experts said Wednesday.
The findings, from preliminary research by the team of South African scientists who identified the variant dubbed 501Y.V2, raise hopes that vaccines modelled on the strain could protect against future mutations.
Identified late last year, the variant fuelled South Africa’s second wave of infection and delayed the start of vaccinations in February.
Scientists said Wednesday plasma collected from people infected with the variant had “good neutralising activity”, including against “first wave” viruses and potentially other variants of concern.
After the antibodies were tested against the original strain and another identified in Brazil, “results are showing a clear sense of direction”, virologist Tulio de Oliveira said in a video conference.
Medrxiv preprint “Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma”
Denmark’s SSI: The Technical University of Denmark, DTU, has found a case of the P1 variant, which was originally detected in Brazil.
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.
“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).
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.
An analysis of 500 samples collected by the new RT-PCR test detected that the P1 line, discovered in Amazonas, has at least twice the viral load found in the others.
According to researcher Felipe Naveca, from the Leônidas & Maria Deane Institute (ILMD / Fiocruz Amazônia), responsible for the study, this is a possible explanation for why the P1 variant is more contagious than the other variations of the virus.
Analysis was performed with samples from different lineages, all from the state of Amazonas, and the results of the positive tests for P1 were compared with those presented by the other variants, in tests carried out between December 2020 and the end of January 2021.
“After using this real-time RT-PCR test, we were able to show that the detectable viral load in the nasopharyngeal secretion of patients with P1 is statistically higher than that of non-P1 patients. Perhaps this is the explanation related to the greater transmission. At least in our data, statistical support for that ”, says Naveca.
Here we report a preliminary genomic analysis of SARS-CoV-2 B.1.1.28 lineage circulating in the Brazilian Amazon region and their evolutionary relationship with emerging and potential emerging SARS-CoV-2 Brazilian variants harboring mutations in the RBD of Spike (S) protein.
Phylogenetic analysis of 69 B.1.1.28 sequences isolated in the Amazonas state revealed the existence of two major clades that have evolved locally without unusual mutations in the S protein from April to November 2020. The B.1.1.28 viruses harboring mutations S:K417N, S:E484K and S:N501Y, recently detected in Japanese travelers returning from Amazonas, branched within one of the Amazonian B.1.1.28 clades here identified, suggesting that these sequences could be representatives of a novel (unreported) emerging Brazilian clade, here designated B.1.1.28(K417N/E484K/N501Y). Our analysis also confirms that the putative novel clade B.1.1.28(K417N/E484K/N501Y) detected in Japanese travelers did not evolve from the clade B.1.1.28(E484K) recently detected in Rio de Janeiro and other Brazilian states, but both variants arose independently during the evolution of the B.1.1.28 lineage.
Clinical trials of the all-Italian anti Covid-19 vaccine has started. The vaccine is conceived by Takis of Castel Romano (Rome) and developed in collaboration with Rottapharm Biotech of Monza.
The first healthy volunteer of the 80 scheduled for phase 1 was vaccinated today in the San Gerardo hospital in Monza, one of the three Italian centers that, in collaboration with the University of Milan-Bicocca.
The clinical trials involve the National Cancer Institute Pascale Foundation of Naples and the National Institute of Infectious Diseases Lazzaro Spallanzani of Rome and the San Gerardo Hospital of Monza.
“A variant of coronavirus circulating in Italy since early August 2020 is “very similar to the infamous English variant [B.1.1.7]”.
An ” Italian variant ” discovered in Brescia, “which precedes the variant that emerged only at the end of September in the United Kingdom and then spread to Europe, including Italy, and could also be a precursor”.
This was announced to Adnkronos Salute by Arnaldo Caruso , president of the Italian Society of Virology (Siv-Isv), full professor of Microbiology and Clinical Microbiology at the University of Brescia, director of the Asst Spedali Civili microbiology laboratory.
The variant identified, he explains, “has several points mutation in the Spike protein , the ‘hook’ that the virus uses to attack the receptor present on target cells in our body. Like the English one, the Italian variant also has a mutation in a nerve center of the Spike / cell receptor interaction, more precisely in position 501 ″.
But unlike the Gb mutant, “the Italian variant also has a second mutation in position 493, which makes its Spike protein slightly different from that of the pandemic virus we all know today”.