Preprint: Emergence and spread of a B.1.1.28-derived lineage with Q675H and Q677H Spike mutations in Uruguay

In a previous study we found a sublineage B.1.1.28+Q675H+Q677H with local transmission in Rocha, a Uruguayan department bordering Brazil. This clade probably arose by early November, 2020, and its introduction from other parts of Uruguay seemed like a reasonable hypothesis. To understand whether these sequences were part of a new emergent SARS-CoV-2 lineage broadly disseminated in Uruguay, herein we analyzed the genetic diversity of B.1.1.28 SARS-CoV-2 viruses circulating in different localities by the end of 2020 and first months of 2021.

Preprint: Emergence and spread of a B.1.1.28-derived lineage with Q675H and Q677H Spike mutations in Uruguay 

 

 

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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

 

 

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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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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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Sudden rise in COVID-19 case fatality among young and middle-aged adults in the south of Brazil after identification of the novel B.1.1.28.1 (P.1) SARS-CoV-2 #coronavirus strain

Individuals between 20 and 29 years of age whose diagnosis was made in February 2021 had an over 3-fold higher risk of death compared to those diagnosed in January 2021, while those aged 30-39, 40-49, 50-59 years experienced 93%, 110%, and 80% increases in risk of death, respectively.

Notably, the observed CFR increase coincided with the second consecutive month of declining number of diagnosed SARS-CoV-2 cases. Taken together, these preliminary findings suggest significant increases in CFR in young and middle-aged adults after identification of a novel SARS-CoV-2 strain circulating in Brazil, and this should raise public health alarms, including the need for more aggressive local and regional public health interventions and faster vaccination.

Medrxiv Preprint

 

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PHE: Two cases of Philippines #coronavirus variant P.3 (PHL-B.1.1.28) found in England

“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.”

PHE Press Release

See also: Other reports on the Philippines variant

90 cases of Brazil related #coronavirus variant PHL-B.1.1.28 in The Philippines

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.

Straitstimes.com report

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

 

 

Japan identifies a B.1.1.28 #coronavirus strain with E484K and N501Y mutations from a traveller from the Philippines

The National Institute of Infectious Diseases, Japan, identified a B.1.1.28 strain with E484K and N501Y mutations from a SARS-CoV-2-positive sample collected on February 25, 2020 at a point of entry to Japan from a traveller from the Philippines(virus name : hCoV-19/Japan/IC-0824/2021, GISAID Accession ID: EPI_ISL_1198832) (1).

These mutations are found in known VOCs (501Y.V2, 501Y.V3). This variant isolate also has the P681H mutation in the spike protein as with B.1.1.7 lineage (VOC-202012/01) which is suggested to be associated with increased transmissibility.

34 draft genome sequences of B.1.1.28 lineage with E484K/N501Y mutations have been uploaded to GISAID from the Philippines (1 sequence on February 26, 33 sequences on March 3) .

The Department of Health, Republic of Philippines, published that they found 34 cases with E484K and N501Y mutations on March 2 (1).

This variant isolate does not meet the criteria of VOC as we do not know how widely this variant strain is spreading within the Philippines and whether this variant strain is associated with the recent increase in reported cases in the Philippines. However, this variant strain may be circulating in the Philippines at a certain level as the similar strain has been reported domestically and identified from travelers.

The potential public health impact from this variant strain shall be considered to be equivalent to those from known VOCs as this variant strain shares the same mutations of concern with VOCs

See alsoNew #coronavirus variant with #E484K, #N501Y & #P681H mutations found in the Philippines, designated PHL-B.1.1.28

NIID statement

 

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More #E484K #B1128 #coronavirus co-infections reported in #Brazil

B.1.1.28 (E484K) is able to establish successful coinfection events co-occurring simultaneously with different lineages of SARS-CoV-2.

The novel variant B.1.1.28 (E484K) previously described in Rio de Janeiro is currently spread across the southernmost state of Brazil.

The novel variant VUI-NP13L was also identified by causing a local outbreak in Rio Grande do Sul.

Medrxix paper  – 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

 

 

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New #coronavirus variant with #E484K, #N501Y & #P681H mutations found in the Philippines, designated PHL-B.1.1.28

Here, we describe the emergence of a new SARS-CoV-2 lineage, mainly from the Central Visayas region of the Philippines. This emergent variant is characterized by 13 lineage-defining mutations, including the co-occurrence of the E484K, N501Y, and P681H mutations at the spike protein region, as well as three additional radical amino acid replacements towards the C-terminal end of the said protein. A three-amino acid deletion at positions 141 to 143 (LGV141_143del) in the spike protein was likewise seen in a region preceding the 144Y deletion found in the B.1.1.7 variant. A single amino acid replacement, K2Q, at the N-terminus of ORF8 was also shared by all 33 samples sequenced.

Medrxiv paper  Genome sequencing and analysis of an emergent SARS-CoV-2 variant characterized by multiple spike protein mutations detected from the Central Visayas Region of the Philippines

 

 

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Phylogenetic relationship of #SARSCoV2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein

Here we report a preliminary genomic analysis of SARS-CoV-2 B.1.1.28 lineage circulating in the Brazilian Amazon region and their evolutionary relationship with emerging and potential emerging SARS-CoV-2 Brazilian variants harboring mutations in the RBD of Spike (S) protein.

Phylogenetic analysis of 69 B.1.1.28 sequences isolated in the Amazonas state revealed the existence of two major clades that have evolved locally without unusual mutations in the S protein from April to November 2020. The B.1.1.28 viruses harboring mutations S:K417N, S:E484K and S:N501Y, recently detected in Japanese travelers returning from Amazonas, branched within one of the Amazonian B.1.1.28 clades here identified, suggesting that these sequences could be representatives of a novel (unreported) emerging Brazilian clade, here designated B.1.1.28(K417N/E484K/N501Y). Our analysis also confirms that the putative novel clade B.1.1.28(K417N/E484K/N501Y) detected in Japanese travelers did not evolve from the clade B.1.1.28(E484K) recently detected in Rio de Janeiro and other Brazilian states, but both variants arose independently during the evolution of the B.1.1.28 lineage.

Full Virological.org paper

 

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Genomic characterisation of an emergent #SARSCoV2 lineage in Manaus, Brazil

“We have detected a new variant circulating in December in Manaus, Amazonas state, north Brazil, where very high attack rates have been estimated previously. The new lineage, named P.1 (descendent of B.1.1.28), contains a unique constellation of lineage defining mutations, including several mutations of known biological importance such as E484K, K417T, and N501Y. Importantly, the P.1 lineage was identified in 42% (13 out of 31) RT-PCR positive samples collected between 15 to 23 December, but it was absent in 26 publicly available genome surveillance samples collected in Manaus between March to November 2020.

These findings indicate local transmission and possibly recent increase in the frequency of a new lineage from the Amazon region. The higher diversity and the earlier sampling dates of P.1. in Manaus corroborates the travel info of recently detected cases in Japan, suggesting the direction of travel was Manaus to Japan. The recent emergence of variants with multiple shared mutations in spike raises concern about convergent evolution to a new phenotype, potentially associated with an increase in transmissibility or propensity for re-infection of individuals.”

https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586

 

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