Here we show that even previously infected and fully vaccinated subjects with high anti-S IgG titers are susceptible to infection by VOC, highlighting that immune responses induced by either natural infection or vaccination may not be sufficient to prevent infection by SARS-CoV-2 variants.
For this study we selected 72 SARS-CoV-2 recently tested positive individuals with nasopharyngeal swabs collected between mid-January and March 2021 with SARS-CoV-2 RT-qPCR Ct values <30. These include both cancer patients and healthcare workers (HCW) from the Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil. Of those 72 subjects, six were vaccinated prior the current infection and two out of those six were also reinfection cases. Another three subjects also represented reinfections, showing a previous infection during the first wave of the pandemic in Brazil.
Six HCW included in this study have been fully or partially vaccinated with one of the vaccines available in Brazil, either CoronaVac (Sinovac/Butantã) or ChAdOx1-S/nCoV-19 (AstraZeneca/Oxford/Fiocruz). All six tested positive for SARS-CoV-2 RT-qPCR after at least one vaccine dose and reported mild symptoms during infection.
Monitoring in Rio de Janeiro, Brazil, has identified a possible new Sars-Cov-2 lineage, originating from P.1.1.28, in the region of Barra Mansa and Porto Real, on the border with the State of São Paulo, and which has only now been called P5. This strain has, among others, two mutations in the Spike protein (E484Q and N501T) that may be associated with escape from the immune system and with virus transmissibility. The discovery was widely reported in newspaper and television news throughout the week.
The results also describe the descendant lineage of VOC gamma (P.1) which was named P.1.2. This strain was initially found in the northern region of the state and is now widespread in all regions of the state of Rio and other states. Monitoring data still show that the P.1 lineage continues to be the most frequent (78%) in the state, and the low frequency of VOC Alpha (B.1.1.7) and the decline of P.2 since November of the year past.
According to Ana Tereza Vasconcelos, from the National Laboratory for Scientific Computing (LNCC), real-time municipal monitoring carried out by Rio de Janeiro is extraordinary for Brazil, and is within the recommendations of the World Health Organization, which recommends 18 days as optimal interval between the release of new data. Of the 92 municipalities in Rio de Janeiro, 91 are already being monitored. From March to June 2021, more than 2,300 samples have already been sequenced and processed on the LNCC supercomputer Santos Dumont, an institution linked to the Ministry of Science, Technology and Innovation (MCTI). Only the municipality of Comendador Levi Gasparian has not yet collected samples.
The data are from patients with a confirmed diagnosis of SARS-CoV-2 infection monitored in reference centers and hospitals in the State of Rio de Janeiro. Reports are issued every 15 days with updated data from 380 samples sequenced in the period and which are immediately available on the website http://www.corona-omica.rj.lncc.br/#/ .
The Brazilian Society of Virology (SBV) yesterday, May 25, confirmed the identification of a new Brazilian coronavirus strain, denominated P4. According to the SBV, the variant has the L452R mutation in the S protein of SARS-CoV-2. According to the SBV, the new variant has been circulating in the region of the São Paulo cities of Mococa, Caconde, and Itapira (close to the border with Minas Gerais), and also in the region of Porto Ferreira .
The L452R mutation in the S protein of SARS-CoV-2 is found in all three sub-lineages of the Indian variant B.1.617 – B.1.617.1, B.1.617.2 and B.1.617.3. There is still no data on whether the new P.4 strain is more transmissible or more lethal than other strains.
The variant of the SARS-Cov-2 coronavirus was detected for the first time in a sample taken in the municipality of Mococa, which is located in the northeast of the state of Sao Paulo.
In addition to Mococa, coronavirus cases caused by the P.4 strain have been registered in municipalities such as Cesário Lange, Porto Ferreira, Santa Cruz das Palmeiras, Tambaú, Itirapina, Rio Claro, Araras, Sumaré, Caconde, Iperó, Capão Bonito , São Miguel Arcanjo, Itapetininga y Descalvado , all located in Sao Paulo.
The highest ever daily country case figure for coronavirus on Planet Earth was recorded in The Seychelles in May 2021. The Seychelles daily case figure, adjusted for population, reached an astonishing 4,083 cases per million.
What is also surprising is that many of the countries on the list with the highest daily case rates also have excellent vaccination rates (see below). The Seychelles, for example, has vaccinated more than 60% of its population.
The reasons behind some of the high daily case numbers are given in articles we have previously published and have linked to below.
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.
Local TV report on Brazilian variant P.1.2 : https://globoplay.globo.com/v/9499613/ (in Brazilian)
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.”
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.
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.
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.
“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. “
If a picture is worth a thousand words, how much is one simple graph like this worth?
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.
“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
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.
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.
If we’re wrong, drop us a line and we’ll update this post!
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.”