Brazil: new #coronavirus strain P.1.2 confirmed circulating in Rio de Janeiro

The State Department of Health of Rio de Janeiro (SES-RJ) announced the identification of the new variant of the Covid virus in Rio de Janeiro late this morning. The strain received the name of P.1.2, because it is a change that occurred in the P.1 line – which appeared in Manaus.

“The objective of the study is to foresee the evaluation of the epidemiological scenario in the state of Rio de Janeiro to anticipate possible genomic alterations of the already known variants and to prepare the state and the municipalities to face any alteration that may change the pattern of the disease”, he affirmed. the superintendent of Epidemiological Surveillance of the Secretary of State for Health, Mário Sérgio Ribeiro.

Also according to the superintendent, still it is not possible to know whether P.1.2 is more lethal or more transmissible . The epidemiological impact is yet to be assessed.

The technical note of the state presents the genomic study with samples carried out between March 24th and April 16th. The study was carried out in partnership between the Lacen-RJ laboratory and the State Department of Health. According to the City Hall of Rio das Ostras, variants P.1 and P.2 have already been confirmed, previously, in the city.

“The presence of these variants in the municipality and the emergence of a new strain reinforce the importance of surveillance and monitoring of virus dispersions, the need to maintain all measures to prevent contagion and to maintain sanitary barriers”, warned the municipality.

Globo.com report

 

Local TV report on Brazilian variant P.1.2 : https://globoplay.globo.com/v/9499613/ (in Brazilian)

 

Brazil: P.1 mutates into new #coronavirus variant P.1.2

 

 

 

Image by Andrea Meakin from Pixabay

Brazil: P.1 mutates into new #coronavirus variant P.1.2

A new variant of the Brazilian coronavirus has been identified this week, according to Rio de Janeiro health authorities. The P1 Manaus strain seems to have mutated. Hence, the new version has been named P.1.2., scientists in Rio said.

The new variant P.1.2 was identified in 5.85% of the 376 samples taken in 57 municipalities of the state of Rio, second only to São Paulo in the total number of cases nationwide.

“So far it cannot be said that this variant is more contagious or lethal, which is a mutation of P1,” Rio State Health Undersecretary Claudia Mello said in a statement. She also explained that “the new variant was found mainly in the northern region of the state of Rio de Janeiro, but also the metropolitan area and coastal municipalities.”

MercoPress.com report

 

The new variant of Covid-19 was discovered during an investigation to identify which strains of the virus more circulate in the state. P1 remains in almost all regions and P2 in the north and in the lowlands. 376 samples were investigated, from 57 municipalities, selected from genomes sent to the Noel Nutels Central Laboratory (Lacen / RJ), between March 24th and April 16th.

Olhardigital.com report

 

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

 

 

Image by Heiko Behn from Pixabay

Brazil rejects the Russian Gamaleya Vaccine – “still has replication-competent adenovirus in it”

Brazil  have turned down the Russian Gamaleya Sputnik V vaccine.  There are questions raised about the manufacturing and scale-up processes. Anvisa, the Brazilian drug agency, also said that every single lot of the AD5 Gamaleya Sputnik V shot that they have data on appears to still have replication-competent adenovirus in it.

Sciencemag.org report

Brazil Government slides outlining the decision (PDF)

 

Brazil: First confirmed death from #coronavirus REINFECTION reported

A 39-year-old Brazilian man who died of COVID-19 last month was suffering from a second bout of the illness, researchers said on Tuesday, making it the country’s first confirmed death from coronavirus reinfection. Both episodes involved variants with the E484K mutation.

The man, from Campo Bom in the southern state of Rio Grande do Sul, had a history of chronic cardiovascular disease and diabetes. He first tested positive on November 30 but details about his symptoms – if any – are unclear. Genomic sequencing revealed the P.1 variant.

The patient fell ill a second time about 3 months later and tested positive on March 11, according to researchers at Feevale University. His initial symptoms were fatigue and respiratory distress, but his condition worsened and he was transferred to the ICU, where he was intubated and died on March 19.

Genomic sequencing of the sample from the second episode revealed the P.2 variant, which is classified as a Variant of Interest.

 

 

Image by laridra from Pixabay

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

Ireland: 24 cases of P.1, 55 cases of B.1.351 and 3 cases of B.1.617 reported

Director of the National Virus Reference Laboratory Dr Cillian de Gascun said that there have been three cases of the recent variant [B.1.617] first identified in India. Dr De Gascun said at least two of them are associated with travel. He said NPHET does not have any data to determine whether the variant is more transmissible or not, but said at this stage people need to remain vigilant and try to contain it locally.  Separately, 24 cases of the P.1 variant, which was first found in Brazil, have so far been confirmed in Ireland, while 55 cases of B.1.351 South African variant have also been confirmed.

RTE.ie report

 

Image by Christian_Birkholz from Pixabay

Brazil: novel #coronavirus variant VUI-NP13L reported along with 2 cases of coinfection with B.1.1.28

“We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484K) with either B.1.1.248 or B.1.91 lineages. Also, clustering analysis revealed the occurrence of a novel cluster of samples circulating in the state (named VUI-NP13L) characterized by 12 lineage-defining mutations.”

ScienceDirect.com preprint:  Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

 

 

Image by Iszarizal Ismail from Pixabay

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

 

Image by Luciano Teixeira from Pixabay

Brazil’s P.1 #coronavirus variant mutating, may become more dangerous – OLD NEWS?

It’s all over the newspapers today – Brazil’s P1 coronavirus variant mutating, may become more dangerous was Reuters headline – but we think it’s OLD NEWS dating back to January 2021.

We’re pretty sure the newspapers are referring to THIS SCIENTIFIC PAPER from the Fiocruz Institute in Brazil, co-authored by Felipe Naveca, dated 28th January 2021, and mentioned in THIS ARTICLE

If we’re wrong, drop us a line and we’ll update this post!

 

 

Genetic Evidence and Host Immune Response in Persons Reinfected with SARS-CoV-2 #coronavirus in Brazil

A paper to be published in May in the U.S. Centers for Disease Control and Prevention’s (CDC/US) journal Emerging Infectious Diseases (EID) shows that a first exposure to COVID-19 in mild or asymptomatic cases may not produce an immune response, and that a person can reinfect himself or herself with the same variant. The second infection can cause stronger symptoms than the first, the study indicates.

The data shows that for a portion of the population that has the disease in the mild form (in which hospitalization is not required) this does not mean that they will be immune or that a reinfection will evolve in a benign way. The study also indicates that reinfection may be more frequent than assumed.

The case of being infected by the same variant happens because the patient would not have built up an immunological memory. In the case of another strain, it would “escape” surveillance, it would not be recognized by the previously generated memory because it is a little different.

To reach these conclusions, the researchers followed a group of 30 people on a weekly basis from March 2020, at the pandemic start, until the end of the year. Of these, four contracted Sars-CoV-2, and some were infected with the same variant. The researchers then sequenced the virus genome in the case of the first infection and then in the second infection to be able to compare them.

“The gene sequencing method developed by MGI allowed us to detect the virus even in samples with low viral load. Today, Bio-Manguinhos [the Immunobiological Technology Institute] has some of these machines,” says Moreno.

In all four cases, the first infection occurred with mild symptoms. In the second, the symptoms were more frequent and stronger, but did not require hospitalization. “These people didn’t actually have detectable immunity until after the second infection. This leads us to believe that for a population part that had the disease in a mild form, one exposure to the virus is not enough, but more than one, to have a degree of immunity,” says Moreno. “This allows a portion of the population that has already been exposed to sustain a new epidemic.”

Fiocruz Institute, Brazil report

CDC paper

 

 

Photo by D A V I D S O N L U N A on Unsplash

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 

 

 

Image by edufeq03 from Pixabay

Sweden’s daily #coronavirus case rate far higher than Brazil or India

The spread of infection in Sweden on Friday was 625 new confirmed infections per day per one million inhabitants and the spread has increased since April 2 when it was 469 per one million inhabitants. The figures are based on an average over the last seven days.

According to Johns Hopkins University’s figures , the average value for the number of infections in Europe right now is 231 new confirmed cases per day and one million inhabitants – in the USA the figure is 205. Sweden’s figures are thus about three times as high.

Only the two small states of San Marino with 711 and Andorra with 630 new confirmed infected per day per million inhabitants have higher numbers.

Dagens Nyheter report

Graph courtesy of OurworldinData.org

 

Detection of 54 cases of the P.1 variant in Massachusetts in less than a month

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

 

Image by David Mark from Pixabay

Identification of a new B.1.1.33 SARS-CoV-2 Variant of Interest (VOI) circulating in Brazil with mutation E484K and multiple deletions in the Spike protein

Here, we report a new SARS-CoV-2 VOI derived from lineage B.1.1.33, preliminary designated as PANGO lineage N.10, harboring 14 lineage defining mutations. It displays as the most remarkable genetic changes the V445A and E484K mutations in the S protein RBD, several non-synonymous mutations (P9L, I210V, and L212I), and three deletions (∆141-144, ∆211, and ∆256-258) in the S protein NTD, including a truncated NS7b protein due to a frame-shifting deletion. Other five lineage-defining mutations were found among NSP3, NSP5, NSP6, and N. This VOI probably emerged in late December 2020 and comprises a significant fraction (23%) of the SARS-CoV-2 positive cases detected in the Brazilian state of Maranhão (Northeastern region), between January and February 2021.

Virilogical.org preprint

 

Image by José Rauryson Alves Bezerra from Pixabay