UK #coronavirus variant B.1.1.7 may not have evolved spontaneously in the UK or within human populations

“Here we analyzed 454,443 SARS-CoV-2 spike genes/proteins and 14,427 whole-genome sequences. We demonstrated that the early variant B.1.1.7 may not have evolved spontaneously in the United Kingdom or within human populations. Our extensive analyses suggested that Canidae, Mustelidae or Felidae, especially the Canidae family (for example, dog) could be a possible host of the direct progenitor of variant B.1.1.7.”

Biorxiv preprint: Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2

 

 

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Sweden: so much for Herd Immunity and Light Touch pandemic policies

“Instead of following evolving evidence, the [Swedish] FHM has doubled down and defended its approach without reconsidering the assumptions on which the failed national approach is based. It has downplayed the roles of asymptomatic spread, aerosol transmission, children as potential source of infection, and the use of face masks. It has maintained an approach that mainly builds on recommendations to take voluntary actions, guided (in our view) more by public opinion than by sound public health policy. “

Lancet article

 

If a picture is worth a thousand words, how much is one simple graph like this worth?

Graph courtesy of OurWorldinData.org

UK: #coronavirus vaccine breakthrough cases reported with B.1.351 and B.1.1.7 variants

People in the UK have been infected with Covid-19 more than once thanks to catching different variants of the coronavirus. Dr Susan Hopkins, chief medical adviser for NHS Test and Trace, said there had been cases where people had become reinfected by different strains of the coronavirus. “We have seen some people who have had their first dose of vaccine who have had the South African variant and the variant that arose in Kent,” she told BBC’s the Andrew Marr show. “You can see that they’re not as good against the South African variant as they are against our own (variant) B117 at preventing infection and transmission.”

KentLive.new report

 

 

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India: double mutant coronavirus variant B.1.617 outcompeting B.1.1.7 UK variant

Data from Outbreak.info suggests that the B.1.617 “double mutant” variant is outcompeting the UK variant B.1.1.7 in India – the B1617 variant is now being detected in nearly twice as many sequences as the UK variant in 7 day rolling average of percent sequences with mutations

Graphs & data courtesy of Outbreak.info

USA: about 60 household pets confirmed positive for #coronavirus in Texas study

Researchers at Texas A&M’s Veterinary Medicine and Biomedical Sciences department have confirmed a cat and dog living in the same house have contracted the UK variant of COVID-19 B.1.1.7.  All of the animals enrolled in their study, about 450 so far, live in Brazos County and live inside homes where a human tested positive for COVID-19. About 60 animals have been confirmed with COVID-19, and a quarter of those animals showed mild symptoms like lack of energy, sneezing and diarrhea. All of the pets infected have recovered.

ABC13.com report

 

 

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Brazil: rapid spread and high impact of the #coronavirus VOC P.1 in Sao Paulo – March 2021

Here, we show evidence of how fast the VOC P.1 has spread in the most populated city in South America – Sao Paulo.  From March 1st to March 15th, 427 nasopharyngeal samples were collected from 245 HP and 125 from HCW outpatients (25.5% and 23.2% of positivity rate, respectively). We then selected 60 samples with Ct value ≤ 30 (38 samples from HP, and 22 from HCW). All HCW presented only mild symptoms and did not need hospitalization.

Of the 60 selected samples, 52 whole genome sequences were generated (30 from HP and 22 from HCW) following the sequencing protocol using the Illumina MiSeq platform and the analysis pipeline described by Resende et al (8). The SARS-CoV-2 lineages were classified by the PANGO lineages nomenclature (9). Genome sequences generated have been deposited at the EpiCoV database on GISAID https://www.gisaid.org/) under accession numbers EPI_ISL_1464630 to EPI_ISL_1464677.

Of the 52 sequenced samples, 44 (84.4%) were identified as VOC P.1;  5 (9.2%) as VOI P.2; 1 (1,9%) as B.1.1.7, and 2 (3,8%) B.1.1.28.

The most notable variants circulating in the second wave, including B.1.1.7 (detected first in the United Kingdom) and B.1.1.351 (detected first in South Africa), and P.1, are related to an increase of transmissibility (2,10). Interestingly, the P.1 variant was first identified in the State of Amazonas, about 3,800 kilometers apart from São Paulo (5). It is evident that the P.1 variant prevailed during the first two weeks of March, showing a regular distribution among HP and HCW with no difference in terms of age, sex, vaccination, and outcome (Table). From the first to the second weeks of March, we observed a higher frequency of P.1 (78.6% and 91.7%, respectively). In this survey, only one sample from a HP was identified as VOC B.1.1.7. The other two samples were identified as B.1.1.28, a widely spread lineage during the first wave in Brazil.

There is a broad discussion about whether the available vaccines against SARS-CoV-2 will be less effective at preventing infection with the emerging variants (10). In this work, 14 samples (26.9%) of the 52 sequenced samples were from individuals that had received at least one dose of vaccine, ChAdOx1-S/nCoV-19 (n=2) or SINOVAC (n=26). Although they were vaccinated, they could not be considered immunized, regarding the days after vaccination.

Among the hospitalized patients, 19 (63%) were admitted to the intensive care unit, from which nine were discharged and ten died. Comparing the RT-PCR Ct values of all attended patients since the first wave, we did not observe any difference in the Ct mean values with those of P.1 (data not shown). May 2020 registered the peak of number of positive cases with a Ct mean of 23.6. Now, as of April 2021, we are facing a rise in the number of cases. However, the Ct mean was 24.9, which may indicate that the spread of P.1 does not contribute to an actual increase in the viral load.

Medrixiv preprint

 

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India: Maharashtra #coronavirus lockdown announced

The Maharashtra government has imposed lockdown-like curbs in the state from 8pm 14th April 2020. Section 144 has been imposed in the state and only essential services will be allowed for the next 15 days. The CM has also said he will request PM Modi to direct air force to help the state meet its oxygen requirements. Public transport will continue to function only for essential workers and in emergency and for essential activities for general public. No religious, social, cultural or political functions allowed.

TimesofIndia.com report

 

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Boris Johnson: “many more people will lose loved ones to #coronavirus”

12th March 2020 – Boris Johnson: “many more people will lose loved ones to coronavirus” (Guardian).       

13th April 2021 – Boris Johnson:  “sadly we will see more hospitalisation and deaths” (Guardian)

16th December 2020: Jacinda Ardern reveals the moment she chose her Covid-19 elimination strategy for New Zealand

 

Identification of a novel #coronavirus lineage harboring E484Q and N501T spike mutations in Minas Gerais, Southeast Brazil

We report a cluster of two sequences characterized by a unique array of 18 mutations, including new non-synonymous changes in the same critical spike amino acid positions, E484Q and N501T. This lineage seems to have emerged independently from the nationally widespread B.1.1.28, as previously reported for P.1 and P.2, and adds up to the composition of a complex epidemiological scenario of the SARS-CoV-2 pandemic in Brazil.

Our analysis revealed the circulation of a putative new variant derived from lineage B.1.1.28, and represented by two genome sequences in our dataset, LBI215 (complete, 99.81% 10x genome coverage, 98.07% 100x genome coverage, average sequencing depth: 1532x, pangolin original classification: B.1.235) and LBI218 (partial, 76.20% 10x genome coverage, 57.45% 100x genome coverage, average sequencing depth: 595x, pangolin original classification: B.1.1.94). These two sequences form a well-supported (SH-aLRT = 100) monophyletic clade characterized by a unique set of 18 nucleotide mutations.

Beyond harboring multiple exclusive synonymous (C1627U, A10888G, C12664U, C24904U, C27807U, A28271U) and non-synonymous (G5180A: ORF1ab D1639N, G9929A: ORF1ab D3222N, G23012C: Spike E484Q, A23064C: Spike N501T, C24374U: Spike L938F, G24410A: Spike D950N, C28311U: Nucleocapsid P13L) SNPs, this lineage also possesses mutations present in other VOCs: deletion 11288-11296 (ORF1ab 3675-3677 SGF; shared by P.1, B.1.1.7 and B.1.351), C21614U (Spike L18F, P.1) and C28253U (Synonymous, P.2). Two additional deletions are present in these sequences: deletions 28881-28889 (Nucleocapsid 203-206 RGTS(T)) and 29581, which causes a frameshift mutation in ORF10. Additional mutations covered only in the LBI215 genome include: G3617A, ORF1ab V1118I; C21846T, spike T95I; deletion 21986-21991, Spike 142/143 GV; T23542C, synonymous. To ascertain that these mutations were not assembly artifacts, we confirmed their presence in the raw sequencing data .

Virological.org preprint : Increasing frequency of SARS-CoV-2 lineages B.1.1.7, P.1 and P.2 and identification of a novel lineage harboring E484Q and N501T spike mutations in Minas Gerais, Southeast Brazil

 

Original press story: UFMG scientists announce they have discovered a new variant of the coronavirus 

 

 

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Evidence for increased vaccine breakthrough rates of #coronavirus variants of concern in BNT162b2 Pfizer-BionTech mRNA vaccinated individuals

Here, we performed a case-control study that examined whether BNT162b2 (Pfizer-BionTech) vaccinees with documented SARS-CoV-2 infection were more likely to become infected with B.1.1.7 or B.1.351 compared with unvaccinated individuals.

Vaccinees infected at least a week after the second dose were disproportionally infected with B.1.351 (odds ratio of 8:1). Those infected between two weeks after the first dose and one week after the second dose, were disproportionally infected by B.1.1.7 [UK variant] (odds ratio of 26:10), suggesting reduced vaccine effectiveness against both VOCs under different dosage/timing conditions. Nevertheless, the B.1.351 [SA variant] incidence in Israel to-date remains low and vaccine effectiveness remains high against B.1.1.7, among those fully vaccinated. These results overall suggest that vaccine breakthrough infection is more frequent with both VOCs, yet a combination of mass-vaccination with two doses coupled with non-pharmaceutical interventions control and contain their spread.

Medrxiv preprint

 

Photo by Hennie Stander on Unsplash

Children now playing ‘huge role’ in spread of #coronavirus variant B.1.1.7

Dr. Michael Osterholm is the Director of the Center for Infectious Disease Research and Policy at the University of Minnesota. “Please understand, this B.1.1.7 variant is a brand new ball game,” Osterholm said on NBC’s Meet the Press. “It infects kids very readily. Unlike previous strains of the virus, we didn’t see children under 8th grade get infected often or they were not frequently very ill, they didn’t transmit to the rest of the community. Anywhere you look where you see this emerging, you see that kids are playing a huge role in the transmission of this,” Osterholm said. “All the things that we had planned for about kids in schools with this virus are really no longer applicable. We’ve got to take a whole new look at this issue.”

ABC7Chicago.com report

 

 

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ONS: Prevalence of Long Haul symptoms following #coronavirus (COVID-19) infection in the UK

Among a sample of over 20,000 study participants who tested positive for COVID-19 between 26 April 2020 and 6 March 2021, 13.7% continued to experience symptoms for at least 12 weeks. This was eight times higher than in a control group of participants who are unlikely to have had COVID-19, suggesting that the prevalence of ongoing symptoms following coronavirus infection is higher than in the general population.

Over the four-week period ending 6 March 2021, an estimated 1.1 million people in private households in the UK reported experiencing long COVID (symptoms persisting more than four weeks after the first suspected coronavirus (COVID-19) episode that are not explained by something else).

The estimates presented in this analysis relate to self-reported long COVID, as experienced by study participants, rather than clinically diagnosed ongoing symptomatic COVID-19 or post-COVID-19 syndrome. There is no universally agreed definition of long COVID, but it covers a broad range of symptoms such as fatigue, muscle pain, and difficulty concentrating.

Self-reported long COVID symptoms were adversely affecting the day-to-day activities of 674,000 people in private households in the UK, with 196,000 of these individuals reporting that their ability to undertake their day-to-day activities had been limited a lot.

Of people with self-reported long COVID, 697,000 first had (or suspected they had) COVID-19 at least 12 weeks previously, and 70,000 first had (or suspected they had) COVID-19 at least one year previously.

Prevalence rates of self-reported long COVID were greatest in people aged 35 to 69 years, females, those living in the most deprived areas, those working in health or social care, and those with a pre-existing, activity-limiting health condition; however, it is not possible to say whether these patterns are because of differences in the risk of coronavirus infection or susceptibility to experiencing long COVID following infection.

These estimates provide a measure of the prevalence of self-reported long COVID across the whole population, and reflect both the risk of being infected with coronavirus and the risk of developing long COVID following infection; to investigate the second of these components, we examined the duration of self-reported symptoms following confirmed infection.

Of study participants who tested positive for COVID-19, symptom prevalence at 12 weeks post-infection was higher for female participants (14.7%) than male participants (12.7%) and was highest among those aged 25 to 34 years (18.2%).

ONS Study

 

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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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