key: cord-0709157-5ogges89
authors: Campos, G. S.; Giovanetti, M.; de Moraes, L.; da Hora, H. S.; Alcantara, K. M.; Sardi, S. I.
title: Genomic monitoring unveils a high prevalence of SARS-CoV 2 Omicron Variant in vaccine breakthrough cases in Bahia, Brazil
date: 2022-02-21
journal: nan
DOI: 10.1101/2022.02.16.22271059
sha: faba9448654ce9dbd23ee2e705fc21377cce13c9
doc_id: 709157
cord_uid: 5ogges89

Genome sequencing proved to be an excellent tool to monitor the molecular epidemiology of the disease caused by SARS-CoV-2, i.e., coronavirus disease (COVID-19). Some reports of infected, vaccinated individuals have aroused great interest because they are primarily being infected with circulating variants of concern (VOCs). To investigate the cases of infected, vaccinated individuals in Salvador, Bahia, Brazil, we performed genomic monitoring to estimate the magnitude of the different VOCs in these cases. Nasopharyngeal swabs from infected (symptomatic and asymptomatic), fully vaccinated individuals (n=29) who were of varying age and had RT-qPCR Ct values of [≤]30 were subjected to viral sequencing using Nanopore technology. Our analysis revealed that the Omicron variant was found in 99% of cases and that only one case was due to the Delta variant. Infected, fully vaccinated patients have a favorable clinical prognosis; however, within the community, they become viral carriers with the aggravating factor of viral dissemination of VOCs not neutralized by the vaccines.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes COVID- 19 , a disease that emerged in December 2019 in Wuhan, China, fueled worldwide efforts to develop vaccines to control the rapid spread of infection.

Currently, there are several vaccines against SARS-CoV-2 approved by the World Health Organization (WHO) 1 . However, the viral replication of this RNA virus has general characteristics common to other RNA viruses; the high mutation rate allows it to generate new viral variants to improve its chances of survival in the host and escape to immune detection 2 .

It has been shown that SARS-CoV-2 vaccines do not protect against viral infection, although they significantly reduce morbidity and mortality in infected patients. Moreover, the neutralizing antibodies persist for no more than 4 or 5 months, even with a full twodose regimen 3 . These factors may contribute to the fact that fully vaccinated individuals, as well as those with booster doses, may acquire the infection. Although the clinical situation of the infected patient who is fully vaccinated has a very favorable prognosis, they become a possible viral carrier and can trigger viral dissemination within the community 4, 5 .

Recent studies of infected, vaccinated individuals have generated notable interest because they show that these individuals can primarily be infected with the circulating . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity.

is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 21, 2022. ; https://doi.org/10.1101/2022.02.16.22271059 doi: medRxiv preprint variants of concern (VOCs), such as Omicron (B.1.529). This variant is more aggressive, with greater transmissibility and infectivity compared to the Delta variant 6 .

Here, we conducted a genomic study to estimate the magnitude and range of SARS-CoV-2 VOCs in cases of infected (symptomatic and asymptomatic), fully vaccinated individuals.

Patients (n=29) of any gender or age group, symptomatic or not, after consenting, clinical information and oropharyngeal and nasal swab were collected at the Laboratory of 

This research was reviewed and approved by the Ethical Committee of the Federal University of Bahia (CAAE 30687320.9.0000.5662), and informed consent of all participating subjects or their legal guardians have been obtained.

Samples (n=29) were selected for sequencing based on the Ct value (≤30) and availability of epidemiological metadata (sex, age, residence in Salvador, symptoms, etc.) ( Table 1 ). The preparation of SARS-CoV-2 genomic libraries was performed using the nanopore sequencing technology 8 . The SuperScript IV Reverse Transcriptase kit (Invitrogen, USA) was initially used for cDNA synthesis, following the manufacturer's instructions. The cDNA generated was subjected to multiplex PCR sequencing using the is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Oxford Nanopore Technologies, UK). Sequencing libraries were loaded into an R9.4 flow cell (Oxford Nanopore Technologies, UK). In each sequencing run, we used negative controls to prevent and check for possible contamination with less than 2% mean coverage.

The fast5 files generated during sequencing were basecalled under the high-accuracy model performed by Guppy v.6.0.1 (Oxford Nanopore Technologies, UK). The basecalled fastQ files with a minimum Q score of 7 were selected for subsequent trim adaptor and demultiplex processes performed by Guppy v.6.0.1. Furthermore, the fastQ files were submitted to the ARTIC Network's field bioinformatics pipeline v.1.2.1 9 . Briefly, a length filtering was performed to remove additional chimeras using artic guppyplex. 

Lineage assignment was performed using the Pangolin lineage classification software tool 15 is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint 

In this study, all individuals (n=29) were vaccinated with a complete two-dose regimen, except for four 7-and 11-year-olds who were not vaccinated ( Table 1 ). The symptoms self-referred by participants were mild or asymptomatic, without the need for hospital care. The RT-qPCR Ct values varied between 14.6 and 27.2, even in individuals who declared themselves as asymptomatic (Fig. 1) is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 21, 2022. It is important to acknowledge the limitations of these vaccines and to urgently develop new vaccines to emergent VOCs, as is the case of the vaccine for Influenza; going through new doses of the same vaccines is "more of the same".

Measures to control the use of face masks, social distancing, and crowd avoidance continue to be effective, but these need to be combined with new immunogens that prevent viral infection (an elementary concept for the approval of vaccines for widespread use).

This work was supported by Fundação de Apoio a Extensão e Pesquisa -Bahia-Brazil is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 qRT-PCR CT value Sample Symptomatic

Asymptomatic Unvaccinated . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity.

is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 21, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 21, 2022. ; https://doi.org/10.1101/2022.02.16.22271059 doi: medRxiv preprint

World Health Organization. WHO Coronavirus Disease (COVID-19)

Mutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity

Correlation of SARS-CoV-2-breakthrough infections to time-fromvaccine

Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the

Vaccine Breakthrough Infections with SARS-CoV-2 Variants

Omicron (B.1.1.529): Infectivity, vaccine breakthrough, and antibody resistance

National Center for Immunization and Respiratory Diseases (NCIRD) D of VD. Novel Coronavirus (2019-nCoV) Real-time RT-PCR Primers and Probes

Genomic epidemiology reveals how restriction measures shaped the SARS-CoV-2 epidemic in Brazil

ARTIC field bioinformatics pipeline

Minimap2: pairwise alignment for nucleotide sequences

Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing

Twelve years of SAMtools and BCFtools. Gigascience

Automated generation of heuristics for biological sequence comparison

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes

Minimap2: pairwise alignment for nucleotide sequences

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

TreeTime: Maximum-likelihood phylodynamic analysis

Waning Immunity after the BNT162b2 Vaccine in Israel

SARS-CoV-2 Omicron Variant Neutralization in Serum from Vaccinated and Convalescent Persons

World Health Organization. WHO Coronavirus Disease (COVID-19)

Increased risk of infection with SARS-CoV-2 Omicron BA.1 compared with Delta in vaccinated

It is made available under a perpetuity.is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint