Epidemiological and Genomic Analysis of Asymptomatic SARS-CoV-2 Infections during the Delta and Omicron Epidemic Waves in São Paulo City, Brazil

Abstract

We examined the asymptomatic rates of SARS-CoV-2 infection during the Delta and Omicron waves in the city of São Paulo. Nasopharyngeal swabs were collected at strategic points of the city (open-air markets, bus terminals, airports) for SARS-CoV-2 RNA testing. Applying the questionnaire, the symptomatic individuals were excluded, and only asymptomatic cases were analyzed. During the Delta wave, a total of 4315 samples were collected, whereas 2372 samples were collected during the first Omicron wave. The incidence of the asymptomatic SARS-CoV-2 infection was 0.6% during the Delta wave and 0.8% during the Omicron wave. No statistical differences were found in the threshold amplification cycle. However, there was a statistical difference observed in the sublineage distribution between asymptomatic and symptomatic individuals. Our study determined the incidence of asymptomatic infection by monitoring individuals who remained symptom-free, thereby providing a reliable evaluation of asymptomatic SARS-CoV-2 carriage. Our findings reveal a relatively low proportion of asymptomatic cases, which could be attributed to our rigorous monitoring protocol for the presence of clinical symptoms. Investigating asymptomatic infection rates is crucial to develop and implement effective disease control strategies.

Keywords: Brazil; SARS-CoV-2; asymptomatic infection; epidemiology; genomic surveillance; molecular testing.

Figure 1

(A) Flowchart illustrating the primary field and laboratory procedures involved in assessing the prevalence of asymptomatic SARS-CoV-2 infection in São Paulo city. (B) Map of São Paulo, presenting the locations of the sampling points. The map features distinct color-coded lines representing the major city regions, grouped together based on neighborhood proximity. The shaded neighborhoods on the map indicate the precise sampling points chosen for data collection and analysis. (C) Image showcasing the collection points for the samples.

Figure 2

Lineage distribution across samplings. Outer circles: genomes obtained from symptomatic individuals (used as background); inner circles: genomes obtained from asymptomatic individuals (from this study). (A—left) Lineage distribution from the Delta wave, containing 23 genomes from asymptomatic individuals and 318 genomes from symptomatic individuals. (A—right) Lineage distribution from the Omicron wave, containing 15 genomes from asymptomatic individuals and 54 genomes from symptomatic individuals. (B) Maximum likelihood tree of genomic sequences from São Paulo city. (B—left) Samples from Delta wave. (B—right) Samples from Omicron wave. Genomes from symptomatic individuals are represented by triangles in the tip of the trees, while asymptomatic genomes are represented by circles, pointed by red arrows.