Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil

Abstract

The introduction of SARS-CoV-2 variants of concern (VOCs) in Brazil has been associated with major impacts on the epidemiological and public health scenario. In this study, 291,571 samples were investigated for SARS-CoV-2 variants from August 2021 to March 2022 (the highest peak of positive cases) in four geographical regions of Brazil. To identify the frequency, introduction, and dispersion of SARS-CoV-2 variants in 12 Brazilian capitals, VOCs defining spike mutations were identified in 35,735 samples through genotyping and viral genome sequencing. Omicron VOC was detected in late November 2021 and replaced the Delta VOC in approximately 3.5 weeks. We estimated viral load differences between SARS-CoV-2 Delta and Omicron through the evaluation of the RT-qPCR cycle threshold (Ct) score in 77,262 samples. The analysis demonstrated that the Omicron VOC has a lower viral load in infected patients than the Delta VOC. Analyses of clinical outcomes in 17,586 patients across the country indicated that individuals infected with Omicron were less likely to need ventilatory support. The results of our study reinforce the importance of surveillance programs at the national level and showed the introduction and faster dispersion of Omicron over Delta VOC in Brazil without increasing the numbers of severe cases of COVID-19.

Keywords: COVID-19; SARS-CoV-2; epidemiologic surveillance; symptoms; variants; viral load.

Figure 1

Descriptive analysis of the study design. (A) Twelve capitals distributed along four macro-regions of Brazil were included in this study. A total of 77,262 samples with confirmed positive COVID-19 diagnoses were evaluated. The blue circle size represents the proportion of positive samples in each Brazilian capital; (B) the cartogram of sample representativeness according to the population of each Brazilian region; (C) the sex and age profile of the study sample (data were grouped by sex and age clusters); and (D) the sex profile by Brazilian capital of the study sample. The gray and magenta bars correspond to men’s and women’s records, respectively.

Figure 2

Monitoring of Delta and Omicron VOCs in Brazil. Delta and Omicron variants were represented by red and dark purple colors, respectively. (A) Percentage of non-SGTF and SGTF samples per epidemiological week in 35,735 samples across Brazil. (B) Absolute numbers of non-SGTF and SGTF profiles in the positive RT-PCR samples per epidemiological week and positive rate; (C) Transition period between non-SGTF and SGTF samples by capital and epidemiological week. Blank spaces indicate the absence of samples in a particular capital within the specified epidemiological week.

Figure 3

Phylogenetic reconstruction of SARS-CoV-2 during the fourth wave of SARS-CoV-2 in Brazil (epidemiological weeks 35/2021 to 09/2022). The dataset was constructed based on the genomes used by Nextclade as references for Omicron classification (n = 1531). Maximum likelihood phylogenetic tree inferred from our dataset to confirm lineage classification. Purple-tipped shapes indicate genomes generated in our study (n = 109). Node values correspond to bootstrap values. The clades corresponding to the variants BA.1, BA.2, BA.4, and BA.5 are highlighted in gray, lilac, pink, and purple, respectively.

Figure 4

Comparative analysis of RT-qPCR Ct values between Delta and Omicron SARS-CoV-2 VOC dominance periods. Colors represent the dominant variant, with a frequency above 90% in the analyzed period, being Delta (red) or Omicron (dark purple). Violin plots displaying the distribution of Ct data according to the predominant lineage for the viral target genes N (A) and ORF1ab (C), and the MS2 internal process control (E). Boxplots display Ct value variation along the epidemiological weeks comprised in the study period (August 29, 2021–March 5, 2022) for the viral target genes N (B), ORF1ab (D), and MS2 internal control (F). A statistical comparison between periods denotes that Omicron VOC might be associated with lower viral loads in the upper respiratory tract than Delta VOC infection. White bars represent the first quartile, the median and the third quartile. Black circles represent the outliers * p < 0.001.

Figure 5

Forest plot of effect sizes measured between Omicron (case) and Delta (control) groups in COVID-19 patients for: (A) need for ventilatory support: 9828 cases and 6488 controls; (B) intensive care unit admission: 9914 cases and 6467 controls; and (C) death: 9815 cases and 6443 controls, in a meta-analysis of 12 different Brazilian capitals according to the periods in which Omicron (case) and Delta (control) VOCs had a minimum prevalence of 90% in each capital city.