“Here we present a case of prolonged infection of greater than 6 months with shedding of high titer SARS-CoV-2 in an individual with advanced HIV and antiretroviral treatment failure. …Through whole genome sequencing at multiple time-points, we demonstrate the early emergence of the E484K substitution associated with escape from neutralizing antibodies, followed by other escape mutations and the N501Y substitution found in most variants of concern.”
The French city of Bordeaux is to fast-track vaccinations for residents in one neighbourhood, opening access the jab for all adults after nearly 50 people tested positive for a “very rare” variant of Covid-19. Labelled VOC 20I/484Q, the strain is related to the British variant B.1.1.7 but with an additional mutation E484Q. The variant has already been identified on a national level in France but it has reportedly been very rare until now. At least 46 people have been infected with the variant in Bordeaux, with mass testing launched on Friday to track down further cases.
“There has never been a cluster like that in the general population,” said Professor Patrick Dehail of the The National Reference Center in Lyon
UPDATE 1: There’s nothing in the latest Epidemiological Update from French Health Department about 20I/E484Q, but 20I/E484K gets a mention:
Le VOC 20I/484K, identifié pour la première fois en Grande-Bretagne suite à l’acquisition par le VOC 20I/501Y.V1 de la mutation E484K, était peu détecté en France jusqu’à la mi-mars. Une transmission communautaire a été rapportée depuis début avril dans plusieurs régions : Bretagne (en particulier à Brest), Ile-de-France et Hauts-de-France. Toutefois, le variant 20I/484K restait très nettement minoritaire par rapport au variant 20I/501Y. Dans les autres régions, aucune évolution notable dans les détections de cas du variant 20I/E484K n’a été observée et le nombre de cas restait faible.
UPDATE 2: The European CDC, which still lists all B.1.617 sub-lineages as Variants of Interest (VOI), not Variants of Concern (VOC), shows the E484Q mutation appears in both B.1.617.1 and B.1.617.3, but NOT B.1.617.2
Well that escalated quickly. It took just a little over one month to do it, but B.1.617.2 is now just hours away from outcompeting B.1.1.7 (aka the UK or Kent variant) on a national scale in Great Britain.
Let’s not forget that B.1.1.7 virtually conquered the globe after being discovered in Britain in September 2020. B117 Infections started to climb rapidly in Britain in December 2020, and it became the dominant sars-cov-2 variant in many countries across the globe shortly thereafter. Now, barely 5 months later, it is being dethroned by a variant that carries neither of the signature sars-cov-2 mutations that were of such concern in the existing VOC’s – E484K and N501Y.
This is the same B.1.617.2 / B.1.1.7 chart for India:
UPDATE 24th May 2021:
A report issued by the UK government’s Scientific Advisory Group for Emergencies (SAGE) found the likelihood that a variant of concern (VOC) that has arisen in humans could infect a rodent and then spread among the animals is high. Researchers say lab evidence indicates that while rats and mice appear unable to contract the most common forms of coronavirus COVID-19, the N501Y spike protein mutation “has an increased affinity” for rodents.
The report said: “There is a plausible pathway for infection of rodents with new variants of concern from infected humans following contamination of an environment. “Experimental evidence has shown SARS-CoV-2 with N501Y has increased affinity for lab rodents and there is nothing to suggest the same would not be true for wild rodents.
SAGE: Coronavirus (COVID-19) response, 8 April 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.
1/2 To date, ≥ 24,995 #VariantsOfConcern cases (↑8,131 since Apr.7), including 23,611 (↑8,112) B.1.1.7, 1,039 (↑16) P.1 & 345 (↑3) B.1.351 variants have been reported, with numbers highest in Ontario, Alberta, British Columbia, & Quebec. https://t.co/IHyBa1lpr8
— Dr. Theresa Tam (@CPHO_Canada) April 9, 2021
“For the first time, however, the P.1 variant that originated in Brazil has taken the No. 2 spot. At least 434 people in the United States have been infected with the variant, which has devastated Brazil, with the largest number of cases found in Massachusetts, Illinois and Florida.”
All three global VoCs (B.1.1.7, B.1.351, and P.1) have now been detected in MA. However, unlike B.1.1.7 and B.1.351, P.1 has shown a rapid rise in frequency in the few weeks following its first detection on March 16th, 2021. Phylogenetic analysis of these 54 P.1 genomes from MA, alongside four additional P.1 genomes from neighbouring states (two from Connecticut (CT) and one each from Maine (ME) and Rhode Island (RI)) and 895 other global P.1 sequences from GISAID, 6 1 suggests at least six introductions of P.1 into MA and at least eight introductions of P.1 into the New England region, likely from both international and domestic sources.
Virological.org preprint – Detection of a large cluster and multiple introductions of the P.1 SARS-CoV-2 Variant of Concern in Massachusetts
We report a SARS-CoV-2 lineage that shares N501Y, P681H, and other mutations with known variants of concern, such as B.1.1.7. This lineage, which we refer to as B.1.x (COG-UK sometimes references similar samples as B.1.324.1), is present in at least 20 states across the USA and in at least six countries. However, a large deletion causes the sequence to be automatically rejected from repositories, suggesting that the frequency of this new lineage is underestimated using public data.
Recent dynamics based on 339 samples obtained in Santa Cruz County, CA, USA suggest that B.1.x may be increasing in frequency at a rate similar to that of B.1.1.7 in Southern California. At present the functional differences between this variant B.1.x and other circulating SARS-CoV-2 variants are unknown, and further studies on secondary attack rates, viral loads, immune evasion and/or disease severity are needed to determine if it poses a public health concern.
BiorXiv preprint: A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control
The VOI 19B / 501Y (lineage A.27) has been detected infrequently but regularly in France since January 2021. It represented 1.8% of the interpretable sequences during the Flash # 4 survey versus 0% during the Flash Inquiry # 3. In weeks 10 and 11, respectively 48 and 47 detections of this variant were reported by the 4 national sequencing platforms.
However, several points of attention should be note and justify continuing the reinforced surveillance of this variant. First, it was detected during several clusters, a priori all closed, affecting schools, healthcare (including centers hospitals, SSR and Ehpad) or military, with for some a high number of COVID-19 cases (more around sixty), particularly in Ile-de-France (2 hospital clusters and 8 intra-family clusters), Pays de la Loire (3 clusters), Brittany (1 cluster in Morbihan) and Nouvelle-Aquitaine (6 clusters in Dordogne).
Community transmission of this variant is suspected in at least two departments (Seine-et-Marne et Dordogne), and additional investigations are currently being carried out by the ARS concerned, in conjunction with SpF and CNR, to characterize this signal. In addition, three cases considered as probable re-infections were identified with confirmation of infection with this variant during the second episode, without it being possible to date to estimate the frequency of re-infections with this variant, nor to compare it with that of other viral strains circulating in France.
Data is still lacking at this stage on the clinical features of infection with this variant, but we did not detect a signal in favor of significant impact on its transmissibility or increased severity of infection caused by this variant. The strengthening of the surveillance of this variant should be able to more precisely document its characteristics, which will be noted to you when additional data becomes available.
French Health Department – Risk analysis related to emerging variants of SARS-COV-2 (PDF)
Approximately 40% of cases of the new coronavirus in Lima have been due to the P.1 Brazilian variant of this disease, according to a study carried out by the Peruvian National Institute of Health (INS).
This was indicated in a press conference by the Minister of Health, Óscar Ugarte . He added that the advance of this variant that has already passed through Loreto and Huánuco is being determined .
“This INS study is extremely important because it has made it possible to identify, through a sampling throughout Lima, that the main variant that causes COVID-19 today in a percentage of 40% is the Brazilian variant,” he said.
Genetic sequencing of positive COVID-19 cases in the past week in Barnstable County, Cape Cod, has resulted in the identification of 50 cases of the P.1 virus variant that originated in Brazil, according to the state Department of Public Health. That’s all but seven of the 57 cases of P.1 that have been detected statewide, the DPH said. The state’s first case, announced March 16, was a Barnstable County woman in her 30s.
“We are currently investigating a significant #COVID19AB outbreak in Alberta involving P.1 variants of concern (the variant that originated in Brazil), linked to a returning traveller.”
We are currently investigating a significant #COVID19AB outbreak in Alberta involving P.1 variants of concern (the variant that originated in Brazil), linked to a returning traveller. (1/4)
— Dr. Deena Hinshaw (@CMOH_Alberta) April 3, 2021
I also want to update Albertans on the #COVID19AB outbreak involving P.1 variants of concern. At this time, the outbreak appears linked to a large employer with multiple sites across Western Canada. (4/10)
— Dr. Deena Hinshaw (@CMOH_Alberta) April 5, 2021