New Variant Covid-19 VUI 202012/01

[Woodchopper]

Genomic Evidence of a Sars-Cov-2 Reinfection Case With E484K Spike Mutation in Brazil

To date, uncertainty remains about how long the protective immune responses against SARS-CoV-2 persists and the first reports of suspected reinfection began to be described in recovered patients months after the first episode. Viral evolution may favor reinfections, and the recently described spike mutations, particularly in the receptor binding domain (RBD) in SARS-CoV-2 lineages circulating in the UK, South Africa, and most recently in Brazil, have raised concern on their potential impact in infectivity and immune escape. We report the first case of reinfection from genetically distinct SARS-CoV-2 lineage presenting the E484K spike mutation in Brazil, a variant associated with escape from neutralizing antibodies.

https://www.preprints.org/manuscript/202101.0132/v1

This of course definitely isn’t the first reinfection case. So no need for alarm as it may not be common to that variant. But something to watch.

[Woodchopper]

Neutralization of N501Y mutant SARS-CoV-2 by BNT162b2 vaccine-elicited sera
https://www.biorxiv.org/content/10.1101 ... 7.425740v1

Pfizer vaccine works on one of the mutations.

[Woodchopper]

Authorities worried UK strain of COVID-19 may be so infectious it broke through normal quarantine protocols
https://www.abc.net.au/news/2021-01-08/ ... r/13039558

Quarantine hotel cleaner in Australia got infected with the UK variant. Was probably infected for days before being tested.

Greater Brisbane area to go into a three day lockdown to try to prevent the spread of the UK variant.
https://www.news.com.au/lifestyle/healt ... 1c8144c098

[Woodchopper]

Investigation of novel SARS-CoV-2 variant
Variant of Concern 202012/01
Technical briefing 3

https://assets.publishing.service.gov.u ... ngland.pdf

[Woodchopper]

Genomic tests on the 24 December 2020 confirmed the presence of the UK variant in Ireland. Further analysis to date has indicated the following cases of the UK variant:
• Week 51 (to 20th Dec): 6 variants in 70 samples or 8.6%
• Week 52 (to 27th Dec): 18 variants in 141 samples or 12.8%
• Week 53/Week 1 (to 3rd Jan): 47 variants in 189 or 24.9%

https://assets.gov.ie/118212/b00522b8-7 ... 185a00.pdf

[Woodchopper]

Genetic variants of the novel coronavirus, including the one found in UK, could impact the performance of some molecular COVID-19 tests and lead to false negative results, the U.S. Food and Drug Administration (FDA) said on Friday.

The agency has alerted clinical laboratory staff and health care providers to the possible false negative results from any molecular test, and has asked them to consider such results in combination with clinical observations, and repeat testing with a different test if COVID-19 is still suspected.

The FDA, however, said the risk that these mutations will impact overall testing accuracy is low.

https://www.reuters.com/article/us-heal ... SKBN29D2IZ

[Woodchopper]

White House Covid task force warns of possible new ‘USA variant’ driving spread

The task force said the recent spike in cases has been at nearly twice the rate seen in the spring and summer seasons, according to the report. The U.S. is recording at least 228,400 new Covid-19 cases and at least 2,760 virus-related deaths each day, based on a seven-day average calculated by CNBC using Johns Hopkins University data. The U.S. reported its deadliest day Thursday with more than 4,000 deaths.

“This acceleration suggests there may be a USA variant that has evolved here, in addition to the UK variant that is already spreading in our communities and may be 50% more transmissible,” the report said. “Aggressive mitigation must be used to match a more aggressive virus; without uniform implementation of effective face masking (two or three ply and well-fitting) and strict social distancing, epidemics could quickly worsen as these variants spread and become predominant.”

https://www.cnbc.com/2021/01/08/white-h ... pread.html

Speculative so far.

[Brightonian]

South African variant discovered in Ireland

[Woodchopper]

Genetic Variants of SARS-CoV-2—What Do They Mean?
https://jamanetwork.com/journals/jama/f ... le/2775006

Good summary.

[Woodchopper]

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, while lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

https://science.sciencemag.org/content/ ... f2946.full

[Woodchopper]

Ireland's 14-day infection rate has risen 10-fold in the last three weeks to 1,291 cases per 100,000, fueled by the new variant and the reopening of shops, restaurants and relaxing of a ban on household visits ahead of Christmas.

Martin said he was told by Ireland's chief medical officer that the new variant accounted for 45% of the most recent 92 samples than underwent additional testing, compared with 25% of those tested in the week to Jan. 3 and 9% two weeks earlier.

https://news.yahoo.com/incidence-faster ... 58311.html

[Woodchopper]

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.

https://virological.org/t/phylogenetic- ... rotein/585

[Woodchopper]

Article in Russian, via Google Translate a woman with five month long chronic infection was found with Covid that had 18 mutations.
https://ria.ru/20210112/koronavirus-1592672136.html

[shpalman]

4-6 weeks lockdown is nothing like enough to get close to zero, even for the original version. You perhaps don't appreciate how high our cases are.

For the English variant maybe 4 months is needed to get back to test & traceable levels - something like 10% reduction per week.

Maybe it would go down faster if the English lockdown were actually a proper lockdown.

Italy halved its average case rate in 7 weeks or so (which does indeed roughly correspond to 10% per week) since early November; Lombardy's rate is a quarter of what it was at that peak (it's about 120/100,000/week now).

However, it seems to have stopped going down. Statistics are messed up a bit by all the holidays. Some regions, such as Veneto, lost control and had a double peak.

Now there's talk of a variante veneta. Not to be outdone by England, Italy had to have its own damn variant.

[Woodchopper]

COG-UK report on SARS-CoV-2 Spike mutations of interest in the UK 15th January 2021
https://www.cogconsortium.uk/wp-content ... ations.pdf

[Woodchopper]

Emergence of multiple SARS-CoV-2 mutations in an immunocompromised host
https://www.medrxiv.org/content/10.1101 ... 20248871v1

[Woodchopper]

The lethal triad: SARS-CoV-2 Spike, ACE2 and TMPRSS2. Mutations in host and pathogen may affect the course of pandemic
“ dynamics of pandemics are strongly influenced not only by virus variation but also by host genetic background.”
https://www.biorxiv.org/content/10.1101 ... 2.426365v1

[Martin Y]

<edit> quoted wrong link. Nvm.