A-307 Spread Dynamic of SARS-CoV-2 Variants and Related Alterations in Transmission Rates: A National Scale Study

Abstract

Abstract Background In late 2019, the world was surprised by the new coronavirus (SARS-CoV-2), responsible for the COVID-19 pandemic and the ability to develop and share knowledge about SARS-CoV-2 was essential in combat of the pandemic. Genomic surveillance has played a fundamental role in identifying new mutations, detecting emerging variants, and monitoring viral evolution. Although next-generation sequencing (NGS) remains the gold standard for the identification of new variants, this technology is still restricted due to the high cost. Thus, the use of accessible methods for SARS-CoV-2 monitoring is necessary. This study aimed to collect and share monitoring data of COVID-19 in Brazil and to evaluate the dynamics of SARS-CoV-2 variants during the two periods of changes in the epidemiological scenario (second and third pandemic waves) and the transmissibility rates among circulating VOCs. Methods The study evaluated 27 003 samples from all federative units in Brazil between April/2021 and January/2022. Specific primers and probes were used for the mutations K417T/N, L452R, E484K/Q, N501Y, P681R (TaqMan SARS-CoV-2 Mutation Panel), and the SGTF (S-gene target failure) by the TaqPath COVID-19 CE-IVD RT-PCR Kit according to the frequencies of the Gamma, Delta, and Omicron VOCs in the evaluated time. Samples showing an unexpected mutation profile in RT-qPCR genotyping were submitted to NGS. Data for viral targets of about 227 661 positive samples were collected to assess the period of predominance of each VOC as an inference of transmissibility potential. Results Samples were collected in all 27 Brazilian federative units. The replacement of the Gamma by Delta variant occurred in about 5 months, between June and September 2021, when the Delta variant reached 100% of infections. The transition of predominance among the Delta to Omicron variant was only 2 months, demonstrated by the progressive increase of Omicron in November (3.4%), December (67.5%), and January (97%), accompanied by the consequent growth of COVID-19 positive cases in the country. These results reinforce the higher transmissibility of Omicron compared to other variants identified in Brazil. The adopted strategy was able to identify the Gamma, Delta, and Omicron VOCs as well as the presence of other variants in 99.2% of the samples. Only 0.8% of the samples were not characterized and it was submitted to NGS. Conclusion We described a methodology that was able to effectively follow the fast establishment of Omicron VOC related to its higher transmission rates and genomic mutations that explain the highest peak of COVID-19 in our country. This study comprises the largest national-scale of genomic surveillance of SARS-CoV-2, providing information about the virus spread in Brazil.