key: cord-0727015-bte3rwm5
authors: Freire Neto, F. P.; Teixeira, D.; Cunha, D. C. S.; Morais, I. C.; Tavares, C. P. M.; Gurgel, G. P.; Nascimento, S. D.; Santos, D. C.; Sales, A. O.; Jeronimo, S. M. B.
title: SARS-CoV-2 reinfections with BA.1 (Omicron) variant among fully vaccinated individuals in the northeast of Brazil
date: 2022-04-10
journal: nan
DOI: 10.1101/2022.04.08.22272726
sha: 2fa6b06eefa0b4427ccfac7674f06f91ac0f9d28
doc_id: 727015
cord_uid: bte3rwm5

Background: The first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Rio Grande do Norte, northeast Brazil, was diagnosed on March 12, 2020; thereafter, the pattern of COVID-19 followed the multiple waves as seen elsewhere. The waves were mostly due to the SARS-CoV-2 virus mutations leading to emergence of variants of concern (VoC). The introduction of new VoCs in a population context of prior SARS-CoV-2 infections or after vaccination has been a challenge in understanding the kinetics of the protective immune response against SARS-CoV-2 . 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 when the omicron variant was introduced. Methodology/Principal findings: From a total of 172,965 individuals with mild to severe respiratory symptoms, 58,097 tested positive for SARS-CoV-2 between March 2020 through mid-February 2022. Of those previously infected, 444 had documented a second SARS-CoV-2 infection and 9 of these reinfection cases were selected for sequencing. Genomic analysis revealed that virus lineages diverged between primary and the reinfection, with the latter caused by the Omicron (BA.1) variant among individuals fully vaccinated against SARS-CoV-2. Conclusions/Significance: Once all subjects whose samples were sequenced had prior SARS-CoV-2 infection and were also fully vaccinated, our data suggest that the Omicron variant evades natural and vaccine-induced immunities, confirming the continuous need to decrease transmission and to develop effective blocking vaccines.

3 43 Author summary 44 The pattern of the COVID-19 pandemic has been characterized by multiple waves of 45 cases with a variety of outcomes from asymptomatic, to moderate or to severe fatal cases. By 53 Of the reinfection cases, 9 were sequenced and genetic analysis showed that they belong to a 54 BA.1 lineage, which seems to have been introduced multiple times into the region. The primary 55 isolates varied. Thus, our data suggest that the Omicron variant evades immunity provided from 56 either natural infection from any other SARS-CoV-2 variants or from different types of 57 vaccines.

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The copyright holder for this preprint this version posted April 10, 2022. ; https://doi.org/10.1101/2022.04.08.22272726 doi: medRxiv preprint 4 58 Introduction 59 The world has followed the spread of SARS-CoV-2 since 2019 in real time. 

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The copyright holder for this preprint this version posted April 10, 2022. . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 10, 2022. . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 10, 2022. . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 10, 2022. . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted April 10, 2022. . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted April 10, 2022. ; https://doi.org/10.1101/2022.04.08.22272726 doi: medRxiv preprint

between the 2 episodes of COVID-19 ranged between 70 and 584 days, with mild clinical 189 presentation for both infections (Fig 2A). The average between the last vaccination date and 190 the second episode was 86.8 days (± 46.1). The most reported symptoms during both infections 191 were headache

such as hypertension, diabetes mellitus, cancer, and asthma/COPD were not 193 reported among participants and none of them were hospitalized

In order to distinguish between reinfection and long-term viral persistence, we 196 performed a maximum-likelihood (ML) phylogenetic analysis of all SARS-CoV-2 whole 197 genomes from Rio Grande do Norte state, recovered from GISAID on

195 lineage by the Pangolin tool, when the ML tree root was set. The 202 tree topology revealed that all sequences belonged to the variant of concern Omicron (BA.1) 203 lineage and they were clustered in a monophyletic clade while their respective pairs, from the 204 previous SARS-CoV-2 infection

Identification of SARS-CoV-2 reinfection cases in Rio Grande do Norte, Brazil. 209 (A) Primary infection and reinfection and the virus lineages. The figure also shows the time

CoV-2 variants B.1.351 and B.1.1.7

Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral 297 immunity

Increased transmissibility of SARS-CoV-2 lineage B.1.1.7 by age and viral load

. CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)The copyright holder for this preprint this version posted April 10, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 10, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 10, 2022. . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted April 10, 2022. ; https://doi.org/10.1101/2022.04.08.22272726 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)The copyright holder for this preprint this version posted April 10, 2022. ; https://doi.org/10.1101/2022.04.08.22272726 doi: medRxiv preprint Ceará (52 flights); Rio Grande do Norte (20 flights); Paraná (4 flights); Goiás (1 flight); and also Portugal with 22 international flights.. CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)The copyright holder for this preprint this version posted April 10, 2022. ; https://doi.org/10.1101/2022.04.08.22272726 doi: medRxiv preprint