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
On Tuesday, the DGS sent a new protocol to ensure enhanced surveillance of cases of Sars-CoV-2 infection linked to the 20C / H655Y variant, several cases of which were identified in mid-March at the Lannion hospital center (Côtes-d’Armor). The last assessment given on Friday reported 13 confirmed cases (including one spotted in Ile-de-France) with 7 deaths.
The peculiarity of the confirmed cases is that the patients had symptoms suggestive of Covid-19 but an RT-PCR “weakly positive or even negative on the usual nasopharyngeal swabs”, recalls the DGS.
Currently, cases have been confirmed outside of Brittany but all remain linked to Lannion. However, “in the absence of data concerning a possible increased transmissibility of this virus and / or a greater frequency of severe forms, this variant is at this stage classified as a variant to follow (VOI, variant of interest )”, indicates the DGS.
We report a novel severe acute respiratory syndrome coronavirus 2 variant derived from clade 19B (HMN.19B variant or Henri Mondor variant). This variant is characterized by the presence of 18 amino acid substitutions, including 7–8 substitutions in the spike protein and 2 deletions. These variants actively circulate in different regions of France.
We identified a new, previously undescribed variant of SARS-CoV-2 (HMN.19B or Henri Mondor variant) within a cluster of hospital staff in Paris. This variant stems from an older SARS CoV-2 clade, 19B, which emerged in late 2019 but have been rarely detected since early 2020, overtaken by clades 20A, 20B, and 20C, which harbor the D614G substitution believed to improve viral transmission (1). The HMN.19B variant is characterized by the presence of 2 deletions and 18 amino acid substitutions over the entire sequence, including 8 substitutions within the spike protein, some of which are common with other recently described variants, a finding in keeping with the ongoing evolutionary convergence of SARS-CoV-2 variants. The acquisition of spike substitutions, including N501Y and L452R, has been suggested to enhance the interaction of spike with the angiotensin-converting enzyme 2 viral receptor. The resulting substantial fitness acquisition could explain the reappearance of clade 19B
In the 4 weeks after its first detection, our laboratory, which maintains 1 of the 4 national SARS CoV-2 sequencing surveillance platforms in France, found the HMN.19B variant in 12 patients from the greater Paris area
“On 9 March, PHE noted a report of 33 cases of a new variant reported by the Philippines. The variant includes a number of notable mutations including E484K and N501Y, which are found in several other Variants of Concern. PHE has identified 2 cases of this variant in England. One of the cases is linked with international travel and the other is currently under investigation. All appropriate public health interventions are being undertaken.
This variant has been designated VUI-21MAR-02 (P.3). PHE and international partners continue to monitor the situation closely.”
See also: Other reports on the Philippines variant
The Philippines now has all three variants of the coronavirus that have been fuelling record-breaking spikes in infections across the globe, and a Philippine variant (PHL-B.1.1.28) that has the same lineage as the infectious Brazilian variant.
There are currently 177 cases of the British variant and 90 cases of the South African variety in the Philippines.
A fourth variant (PHL-B.1.1.28) that originated in the Philippines itself is also spreading. It was first identified in a Filipino who travelled to Japan. This so-called Philippine variant has the same lineage as the Brazilian strain.
Over 90 cases of this local strain are now being monitored.
See also [HERE]: Japan identifies a B.1.1.28 #coronavirus strain with E484K and N501Y mutations from a traveller from the Philippines
See also [HERE]: New #coronavirus variant with #E484K, #N501Y & #P681H mutations found in the Philippines, designated PHL-B.1.1.28