New Variant Covid-19 VUI 202012/01

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Woodchopper
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Thu Jan 07, 2021 6:56 pm

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.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Jan 08, 2021 11:44 am

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.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Jan 08, 2021 11:50 am

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

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Jan 08, 2021 4:04 pm

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

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

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Jan 08, 2021 4:18 pm

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

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Jan 08, 2021 9:06 pm

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

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Jan 08, 2021 9:08 pm

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.

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Re: New Variant Covid-19 VUI 202012/01

Post by Brightonian » Fri Jan 08, 2021 9:29 pm


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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Jan 08, 2021 9:30 pm

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

Good summary.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Jan 08, 2021 11:15 pm

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

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Jan 11, 2021 7:45 pm

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

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 12, 2021 8:18 am

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

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 12, 2021 9:33 am

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

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sat Jan 16, 2021 6:48 pm

shpalman wrote:
Sat Jan 02, 2021 11:22 am
lpm wrote:
Sat Jan 02, 2021 11:05 am
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.
molto tricky

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 16, 2021 7:01 pm

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

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 16, 2021 8:19 pm

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

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 16, 2021 8:23 pm

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

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Re: New Variant Covid-19 VUI 202012/01

Post by Martin Y » Sat Jan 16, 2021 8:46 pm

<edit> quoted wrong link. Nvm.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 19, 2021 2:57 pm

Preliminary data from South Africa suggests that the novel variant 501.V2 wasn't recognised by antibodies in 21/44 serum samples collected from people infected in the first wave
https://twitter.com/adamjkucharski/stat ... 51840?s=21

Bad news.

We still don’t know whether or to what extent the efficacy of vaccines will be affected. They could well give some immune protection to the SA variant.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 19, 2021 3:08 pm

UK variant in Denmark over the last seven weeks, per cent of tests:
0.2%
0.4%
0.8%
2.1%
2.4%
3.9%
7%

https://covid19genomics.dk/statistics

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 19, 2021 5:18 pm

Comparison of the new variant in the UK, US and Denmark.

https://twitter.com/trvrb/status/135121 ... 45379?s=21

Rate of growth is remarkably consistent. It also seems similar in Ireland. Consistent with it being circa 30-55% more transmissible.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 19, 2021 5:29 pm

Further data on immune responses following the Pfizer mRNA vaccine against pseudo virus bearing Spike protein with mutations in the B.1.1.7 variant (del69/70, del 144/145, N501Y, A570D, P681H, T716I, S982A, D1118H). There is a modest reduction in efficacy of vaccine sera.

Among 15 individuals with neutralisation activity three weeks after the Pfizer mRNA vaccine, 10 showed evidence of reduction in efficacy of antibodies against the B.1.1.7 mutant (Fold change >3). The highest fold change was 6. Median fold change was 3.85 (IQR 2.68-5.28).

These modest changes are what we expected to see given the mutational profiles, esp del 144/145 which is a target region for our antibodies. Vaccines should be highly effective and vaccine coverage is a priority. Full results and methods on Medrxiv in the coming days.
https://twitter.com/guptar_lab/status/1 ... 36675?s=21

Not very bad in its self. This was after the first dose, so a second dose should help. But bad in that it shows what can happen.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Wed Jan 20, 2021 5:21 am

A lab in Italy reported a cluster of the U.K. coronavirus variant. But that wasn’t enough to stop the spread.

The virus hunter saw the apparent pattern come into view over several hours in late December, as he studied genetic sequences from positive coronavirus tests in his region. He found four cases involving the new, highly infectious British variant, in the same hilltop town.

“A cluster,” said Alessio Lorusso, the virologist.
His findings were a rare, initial insight into the mutated forms of the virus reaching new parts of the world. Most countries, including the United States and across Europe, do not perform enough genomic surveillance to adequately track the virus’s changes — to the alarm of disease control agencies, which warn that governments could be blind to dangerous mutations.

But the scenario in Italy’s mountainous center shows how even when a worrisome variant is detected early, governments can miss the narrow window to mount a rapid response and limit the spread. Containment measures come too late, in the wait for more substantial evidence. And the virus races ahead.

Lorusso’s director quickly notified the affected region of the four cases. But it took more than two weeks for any official confirmation to reach the town of Guardiagrele and its population of 9,000. During that time, overall coronavirus cases there tripled, from 35 on Dec. 28 to more than 100 by mid-January. Of those, 29 have been confirmed to involve the British variant

[...]

No targeted restrictions have been imposed on Guardiagrele or the surrounding region of Abruzzo, though there is a plan to soon perform widespread testing.

[...]

“If you don’t act now, in two months, in all of Europe, we’ll have the British variant taking the place of the current ones,” said Walter Ricciardi, a World Health Organization adviser to Italy’s Health Ministry.

He said that if a highly transmissible variant is detected in a particular place, it is important to act quickly, with widespread testing and restrictions on movement.

“You have to immediately lock down the area,” Ricciardi said.

[...]

Italy reported its first detected case involving the British variant on Dec. 20, in a traveler who had arrived from Britain. The government in Rome stopped flights from the United Kingdom the same day.

But even by then, the variant was apparently already circulating in Italy.

Lorusso spotted the initial four cases from Guardiagrele — three within one family — on Dec. 26, and by Dec. 30, according to a document, the lab had informed regional government officials.

Regional officials, in turn, said they needed national government confirmation of the lab results. Into mid-January, the region was insisting there was still no “definitive proof” of a variant that might be spreading differently.

“The region never said to me, ‘Dear mayor, there is a cluster in your town of the most infectious variant, so you’d better put a stop to everything,’ ” said Guardiagrele’s mayor, Donatello Di Prinzio. “Had that been the case, I would have taken all the required actions.”

Instead, after the end of a national holiday lockdown, all of Abruzzo — including his town — landed back in the lightest tier of Italian restrictions, with shops and hair salons open, and restaurants allowed to offered dine-in service until 6 p.m.

Meanwhile, coronavirus infections in the town were rising rapidly, reaching a point far exceeding anything from earlier waves. A local media report pointed to the variant, and there was speculation about it on Facebook. But without official word, the mayor said he didn’t want to be alarmist.

“I only talk when there is data on my hand and official information,” he said.

While he waited, Di Prinzio asked the region to send civil protection officers, who could supplement a depleted local police unit and help enforce basic distancing measures.

Then, on Tuesday, he was invited to a video conference with a provincial official and mayors from seven other towns that were seeing significant case increases. The authorities agreed to launch a mass-testing campaign in those towns, starting in Guardiagrele. It would kick off Jan. 23 — more than three weeks after Lorusso’s initial findings.

One of the provincial officials involved with the health response, Giuseppe Torzi, said “measures need to be stricter” in places with the variant, but the crux of the response would be the same: try to isolate the positive cases and reduce contacts.

“I could list situations where there’s no English variant and yet there’s been a monstrous increase,” Torzi said. “So it’s not as if the other virus is some joke.”

On Friday, Guardiagrele received definitive word of the variant’s arrival, but not because of a national confirmation. Instead, Lorusso’s lab notified the region, as well as a provincial health director, of updated, more extensive findings. Torzi called the mayor, feeling this time no further research was needed.

The province of Chieti, one portion of Abruzzo, had 51 cases of the variant.
Twenty-nine of those were in Guardiagrele.
That news coincided with a national government order that a large part of the country, including the Abruzzo region, would on the basis of infection rates be classified in the middle tier of coronavirus restrictions, which includes the closure of restaurants for in-person dining. Nonessential travel between regions will be banned through mid-February. But there has been no indication that Guardiagrele would be sealed off, as has happened in numerous hot spot Italian towns throughout the past year.
Speaking to The Washington Post by phone on Friday, Di Prinzio said he would redouble his request for residents to wear masks and keep their distance. He’d already closed a market. Nothing else would change. Even if he wanted to impose a lockdown, he said there was little point; other towns might well have the same problem, and it would have to be a coordinated effort.
Another lab doing genomic sequencing, at the University of Chieti, said it had traced a case in one town, San Giovanni Teatino, back to Guardiagrele, carried by a woman who works there.

“For such reason,” the university wrote to the region, “it is possible to hypothesize that in these cases we are witnessing a progressive expansion of such a variant across the territory.”
https://www.washingtonpost.com/world/eu ... story.html

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Wed Jan 20, 2021 5:27 am

Woodchopper wrote:
Tue Jan 19, 2021 2:57 pm
Preliminary data from South Africa suggests that the novel variant 501.V2 wasn't recognised by antibodies in 21/44 serum samples collected from people infected in the first wave
https://twitter.com/adamjkucharski/stat ... 51840?s=21

Bad news.

We still don’t know whether or to what extent the efficacy of vaccines will be affected. They could well give some immune protection to the SA variant.
Small scale, needs more research etc, but worrying:
SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma

SARS-CoV-2 501Y.V2, a novel lineage of the coronavirus causing COVID-19, contains multiple mutations within two immunodominant domains of the spike protein. Here we show that this lineage exhibits complete escape from three classes of therapeutically relevant monoclonal antibodies. Furthermore 501Y.V2 shows substantial or complete escape from neutralizing antibodies in COVID-19 convalescent plasma. These data highlight the prospect of reinfection with antigenically distinct variants and may foreshadow reduced efficacy of current spike-based vaccines.
https://www.biorxiv.org/content/10.1101 ... 8.427166v1

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Wed Jan 20, 2021 5:39 am

mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants
https://www.biorxiv.org/content/10.1101 ... 5.426911v1

Loss of efficacy of RNA vaccines seems relatively mild. Paper concludes that: “Taken together the results suggest that the monoclonal antibodies in clinical use should be tested against newly arising variants, and that mRNA vaccines may need to be updated periodically to avoid potential loss of clinical efficacy.”

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