SARS-CoV-2 reinfections with BA.1 (Omicron) variant among fully vaccinated individuals in northeastern Brazil
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Abstract
The first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in Rio Grande do Norte, northeastern Brazil, was diagnosed on March 12, 2020; thereafter, multiple surges of infection occurred, similar to what was seen elsewhere. These surges were mostly due to SARS-CoV-2 mutations leading to emergence of variants of concern (VoC). The introduction of new VoCs in a population previously exposed to SARS-CoV-2 or after vaccination has been a challenge to understanding the kinetics of the protective immune response against this virus. The aim of this study was to investigate the outbreak of SARS-CoV-2 reinfections observed in mid-January 2022 in Rio Grande do Norte state, Brazil. It describes the clinical and genomic characteristics of nine cases of reinfection that occurred coincident with the introduction of the omicron variant.
Methodology/Principal findings
Of a total of 172,965 individuals with upper respiratory symptoms tested for SARS-CoV-2, between March 2020 through mid-February 2022, 58,097 tested positive. Of those, 444 had documented a second SARS-CoV-2 infection and nine reinfection cases were selected for sequencing. Genomic analysis revealed that virus lineages diverged between primary infections and the reinfections, with the latter caused by the Omicron (BA.1) variant among individuals fully vaccinated against SARS-CoV-2.
Conclusions/Significance
Our findings suggest that the Omicron variant is able to evade both natural and vaccine-induced immunity, since all nine cases had prior natural infection and, in addition, were fully vaccinated, emphasizing the need to develop effective blocking vaccines.
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SciScore for 10.1101/2022.04.08.22272726: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethical Issues: The study protocol was reviewed and approved by the Federal University of Rio Grande do Norte Ethical committee (36287120.2.0000.5537). Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: cDNA synthesis was performed from the extracted RNA using a multiplex polymerase chain reaction (PCR) protocol, producing 98 amplicons across the SARS-CoV-2 genome (https://artic.network/). Table 2: Resources
Software and Algorithms Sentences Resources Read mapping and Consensus calling: All reads were mapped to the reference SARS-CoV-2 genome (GenBank accession number MN908947.3) using … SciScore for 10.1101/2022.04.08.22272726: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethical Issues: The study protocol was reviewed and approved by the Federal University of Rio Grande do Norte Ethical committee (36287120.2.0000.5537). Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: cDNA synthesis was performed from the extracted RNA using a multiplex polymerase chain reaction (PCR) protocol, producing 98 amplicons across the SARS-CoV-2 genome (https://artic.network/). Table 2: Resources
Software and Algorithms Sentences Resources Read mapping and Consensus calling: All reads were mapped to the reference SARS-CoV-2 genome (GenBank accession number MN908947.3) using the BWA-MEM V0.7.12-r1039 [16]. BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)Next, the removal of duplicate reads and the split of reads containing poorly sequenced base was proceeded by the Genomic Analysis-Toolkit (GATK) V4.2.0.0 [17]; the quality of the final mapping process was accessed by Mosdepth [18] and Qualimap V2.2.1 [19]. Qualimapsuggested: (QualiMap, RRID:SCR_001209)The SNV identification was performed by the HaplotypeCaller function from the GATK, followed by the filtration using the VariantFiltration, FilterVcf and SelectVariants, excluding variants with depth lower than 10. GATKsuggested: (GATK, RRID:SCR_001876)Those variants which passed by the depth threshold were annotated using the SnpEff V5.0e [20]. SnpEffsuggested: (SnpEff, RRID:SCR_005191)The sequence consensus calling was performed by the FastaAlternateReferenceMaker function from GATK, and for the final fasta file those positions covered by fewer than 10 reads were replaced by Ns, by using an in-house script written in Python 3.8 (available at GitHub). Pythonsuggested: (IPython, RRID:SCR_001658)Phylogenetics analysis: The 18 genome sequences obtained in this work were aligned to 700 other genome sequences from Rio Grande do Norte, Brazil, obtained from GISAID on January 20, 2022, using the MAFFT v. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Tree topologies were inspected by Figtree v. Figtreesuggested: (FigTree, RRID:SCR_008515)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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