Early detection of SARS-CoV-2 P.1 variant in Southern Brazil and reinfection of the same patient by P.2

Silva, Mariana Soares da; Demoliner, Meriane; Hansen, Alana Witt; Gularte, Juliana Schons; Silveira, Frank Ferreira; Heldt, Fágner Henrique; Filippi, Micheli; Pereira, Vyctoria Malayhka de Abreu Góes; Silva, Francini Pereira da; Mallmann, Larissa; Fink, Pietra; Silva, Luana Letícia da; Weber, Matheus Nunes; Almeida, Paula Rodrigues de; Fleck, Juliane Deise; Spilki, Fernando Rosado

doi:10.1590/s1678-9946202163058

Cited by 30 publications

(20 citation statements)

References 21 publications

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“…The commercial MagMAX™ CORE Nucleic Acid Purification Kit (Applied biosystems™, Thermo Fisher Scientific, Waltham, MA, USA) kit was used to perform viral RNA extraction using the automated equipment KingFisher™ Duo Prime (Thermo Fisher Scientific™). As previously described by Silva et al, (2021) , viral genome sequencing and phylogenetic analysis were carried out. Briefly, reverse transcription reaction was carried out in RNA extracted by SuperScript IV reverse transcriptase kit (Thermo Fisher Scientific, Waltham, MA, USA).…”

Section: Methodsmentioning

confidence: 99%

Early introduction, dispersal and evolution of Delta SARS-CoV-2 in Southern Brazil, late predominance of AY.99.2 and AY.101 related lineages

et al. 2022

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The emergence of Variants of Concern (VOC) presenting an unusual number of new mutations is one of the most remarkable features of SARS-CoV-2. The Delta variant, since its appearance, replaced the VOC Gamma, which was responsible for the major COVID-19 wave in Brazil. In this study, we performed a Delta whole-genome sequencing of 183 samples as part of a major genomic surveillance study performed since the beginning of the pandemic. Here, we showed an emergence, widespread dispersion and consolidation of the Delta variant in Rio Grande do Sul State, completely replacing the Gamma variant in a four to five months period. Performing the phylogenetic and phylodynamic analysis, the majority of the sequences generated herein were classified as AY.99.2, AY.99.2-like and AY.101. AY.99.2 Delta-related lineage has been widely reported in Brazil and in the Americas as well. Altogether, our findings provided a mutational profile of the sequences and presented high substitutions per site in the root-to-tip phylogenetic tree, corroborating studies that show the high mutational rate of SARS-CoV-2 over time.

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Section: Methodsmentioning

confidence: 99%

Early introduction, dispersal and evolution of Delta SARS-CoV-2 in Southern Brazil, late predominance of AY.99.2 and AY.101 related lineages

et al. 2022

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“…Linage B.1.620 was analyzed in Lithuania in March 2021, also known as the Lithuanian strain, it was found in Central Africa, North America, France, and Belgium. In an analysis of the original variant, this lineage revealed 23 substitutions, most of which are discrete mutations ( Silva et al., 2021 ; Korber et al., 2020 ). Lineage B.1.618 was discovered for the first time in October of 2020, this variant contained E484K mutation with many other variations and showed substantial development in West Bengal, India, in April 2021 ( Biswas et al., 2021 ).…”

Section: Sars-cov-2 Vaccine and Variantsmentioning

confidence: 99%

SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines

Singh

Parveen

Yadav

2021

Front. Cell. Infect. Microbiol.

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The emergence of SARS-CoV-2 variants may cause resistance at the immunity level against current vaccines. Some emergent new variants have increased transmissibility, infectivity, hospitalization, and mortality. Since the administration of the first SARS-CoV-2 vaccine to a human in March 2020, there is an ongoing global race against SARS-CoV-2 to control the current pandemic situation. Spike (S) glycoprotein of SARS-CoV-2 is the main target for current vaccine development, which can neutralize the infection. Companies and academic institutions have developed vaccines based on the S glycoprotein, as well as its antigenic domains and epitopes, which have been proven effective in generating neutralizing antibodies. The effectiveness of SARS-CoV-2 vaccines and other therapeutics developments are limited by the new emergent variants at the global level. We have discussed the emergent variants of SARS-CoV-2 on the efficacy of developed vaccines. Presently, most of the vaccines have been tremendously effective in severe diseases. However, there are still noteworthy challenges in certifying impartial vaccines; the stories of re-infections are generating more stressful conditions, and this needs further clinical evaluation.

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“…The lineages of variants of concern, UK B.1.1.7 [38], South African B.1.351 [39], Brazilian P.1 [40] and Indian B.1.617.2 [41], were used to identify the most prevalent mutations for nsp3, nsp12, ORF3a and ORF9b that would be present in at least 75% of the sequences [42] ( Table 1 ).…”

Section: Methodsmentioning

confidence: 99%

Design of Peptide Vaccine for COVID19: CD8+ and CD4+ T cell epitopes from SARS-CoV-2 open-reading-frame protein variants

Parn

Jabbour

Nguyenkhoa

et al. 2021

Preprint

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has challenged public health at an unprecedented scale which has led to a dramatic loss of human life worldwide. To design a protective vaccine against SARS-CoV-2, it is necessary to understand which SARS-CoV-2 specific epitopes can elicit a T cell response and provide protection across a broad population. In this study, PLpro and RdRp, two immunogenic non-structural proteins from an immunodominant gene region ORF1ab, as well as ORF3a and ORF9b are identified as potential vaccine targets against SARS-CoV-2. To select top epitopes for vaccine design, we used various clinical properties, such as antigenicity, allergenicity, toxicity and IFN-y secretion. The analysis of CD8 and CD4 T cell epitopes revealed multiple potential vaccine constructs that cover a high percentage of the world population. We identified 8 immunogenic, antigenic, non-allergenic, non-toxic, stable and IFN-y inducing CD8 proteins for nsp3, 4 for nsp12, 11 for ORF3a and 3 for ORF9b that are common across four lineages of variants of concern: B.1.1.7, P.1, B.1.351 and B.1.617.2, which protect 98.12%, 87.08%, 96.07% and 63.8% of the world population, respectively. We also identified variant specific T cell epitopes that could be useful in targeting each variant strain separately. Including the prediction of mouse MHC affinity towards our top CD8 epitopes, our study revealed a total of 3 immunogenic, antigenic, non-allergenic, non-toxic, stable and IFN-y inducing CD8 epitopes overlapping with 6 antigenic, non-allergenic, non-toxic, stable and IFN-y inducing CD4 epitopes across all four variants of concern which can effectively be utilized in pre-clinical studies. The landscape of SARS-CoV-2 T cell epitopes that we identified can help lead SARS-CoV-2 vaccine development as well as epitope-based peptide vaccine research in the future.

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Early detection of SARS-CoV-2 P.1 variant in Southern Brazil and reinfection of the same patient by P.2

Abstract: This is an open-access article distributed under the terms of the Creative Commons Attribution License.

Cited by 30 publications

References 21 publications

Early introduction, dispersal and evolution of Delta SARS-CoV-2 in Southern Brazil, late predominance of AY.99.2 and AY.101 related lineages

Early introduction, dispersal and evolution of Delta SARS-CoV-2 in Southern Brazil, late predominance of AY.99.2 and AY.101 related lineages

SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines

Design of Peptide Vaccine for COVID19: CD8+ and CD4+ T cell epitopes from SARS-CoV-2 open-reading-frame protein variants

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