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Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-21268286


Immunological assays to detect SARS-CoV-2 Spike receptor binding domain antigen seroconversion in humans are important tools to monitor the levels of protecting antibodies in the population in response to infection and/or immunization. Here we describe a simple, low cost and high throughput Ni2+ magnetic bead immunoassay to detect human IgG reactive to Spike S1 RBD Receptor Binding Domain produced in Escherichia coli. A 6xHis tagged Spike S1 RBD was expressed in E. coli and purified by affinity chromatography. The protein was mobilized on the surface of Ni2+ magnetic beads and used to investigate the presence of reactive IgG in the serum obtained from pre-pandemic and COVID-19 confirmed cases. The method was validated with a cohort of 290 samples and an area under the receiver operating characteristics curve of 0.94 was obtained. The method operated with>82% sensitivity at 98% specificity and was also able to track human IgG raised in response to vaccination with Comirnaty with 85% sensitivity. The IgG signal obtained with the described method was well correlated with the signal obtained when pre fusion Spike produced in HEK cell lines were used as antigen. This novel low-cost and high throughput immunoassay may act as an important tool to investigate protecting IgG antibodies against SARS-CoV-2 in the human population.

Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-21260508


We report a genomic surveillance of SARS-CoV-2 lineages circulating in Parana, Southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Parana in March 2020 were the B.1.1.33 and B.1.1.28 variants. The variants B.1.1.28 and B.1.1.33 were predominant throughout 2020 until the introduction of the variant P.2 in August 2020 and a variant of concern (VOC), P.1, in January 2021. Phylogenetic analyses of the SARS-CoV-2 genomes that were previously classified as the VOC P.1 lineage by PANGO showed that some genomes from February to April 2021 branched in a monophyletic clade and that these samples grouped together with genomes recently described with the lineage P.1-like-II. An extended phylogenetic analysis, including SARS-CoV-2 genomes from all over Brazil, showed that the P.1-like-II lineage appears at a high frequency in the southern region of the country. The P.1-like-II lineage genomes share some, but not all, defining mutations of the VOC P.1. For instance, it has the previously described ORF1a:D2980H and N:P383 L unique mutations and the newly detected ORF1a:P1213 L and ORF1b:K2340N mutations. Additionally, a new mutation (E661D) in the spike (S) protein has been identified in nearly 10% of the genomes classified as the VOC P.1 from Parana in March and April 2021. We also report the identification of the S:W152C mutation in one genome from Parana, classified as the N.10 variant. Finally, we analyzed the correlation between the lineage and the P.1 variant frequency, age group (patients younger or older than 60 years old) and the clinical data of 86 cases from the state of Parana. This analysis does not support an association between the P.1 variant prevalence and COVID-19 severity or age strata. Our results provided a reliable picture of the evolution of the SARS-CoV-2 pandemic in the state of Parana characterized by the dominance of the P.1 strain, as well as a high frequencies of the P.1-like-II lineage and the S:E661D mutations. Epidemiological and genomic surveillance efforts should be continued to unveil the biological relevance of the novel mutations detected in the VOC P.1 in Parana.

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