Omicron is already in all states, according to Fiocruz.

By Denise Assis, 247 - The real-time RT-PCR tests performed in each federative unit end up forming a fundamental database for Fiocruz to monitor the evolution of SARS-CoV-2 and its variants. The act of testing allows for a representative sampling of positive cases. Another source of valuable information is the samples of what the Foundation calls "unusual events," identified by local health surveillance, which allow for the classification and monitoring of variants. There are currently more than a thousand defined lineages of the SARS-CoV-2 virus, but only 5 have been identified as variants of concern, with a significant impact on public health, due to characteristics such as greater transmissibility and infection capacity, greater antibody escape capacity, or a combination of these.

Researchers from the Fiocruz Genomic Network, dedicated to these studies, released data referring to the period from January 14th to 27th. The update describes the situation of SARS-CoV-2 virus lineages and variants in Brazil, considering the results of genomic surveillance produced by the Network and other initiatives. The information is from the Fiocruz News Agency. Based on this data, the researchers point out that, while in December the Omicron variant represented 39,4% of sequenced genomes, in January 2022 this rate reached 95,9%, being found in all regions of the country. The Network's report shows that Omicron completely dominates the epidemiological scenario of Covid-19 in Brazil.

In those two weeks (January 14-27), the Respiratory Virus and Measles Laboratory of the Oswaldo Cruz Institute (IOC/Fiocruz) and units of the Foundation in six states (Amazonas, Ceará, Pernambuco, Paraná, Bahia, and Minas Gerais) produced 3.739 genomes. Each of the Fiocruz sequencing units (in addition to those already mentioned, there is also one in Piauí) serves one or more Federative Units (UF).

Researchers from the Fiocruz Genomic Network point out that all this surveillance monitoring is possible thanks to the partnership and collaboration of the State Public Health Laboratories (LACENs) and the General Coordination of Laboratories of the Ministry of Health. The WHO's GISAID platform for genome repositories also contributes significantly to this real-time data retrieval. 

ViralFlow platform enables focused research.

The report states that the Fiocruz Genomic Network developed the ViralFlow platform, aiming to change the scenario where research groups work in a decentralized manner, using different tools to obtain and analyze sequences. Working with dispersed tools is time-consuming and requires researchers to invest in training to use various services.

Furthermore, in cases where the same patient is infected with two or more variants, the separation and assembly of genomes are not possible using these tools. Developed at Fiocruz Pernambuco, ViralFlow automates several important processes for genomic surveillance and offers a platform for researchers to study multiple aspects of SARS-CoV-2 samples in a centralized and agile manner.

Another innovation, aimed at improving the work of the Fiocruz Genomic Network, is the Helper system, successfully employed in diagnostic assays and inference tests for variant detection. The tool provides greater efficiency in multiple result checks and in the time for registration and release of results (approximately four hours of an analyst's time for each batch of results generated).

The implementation process is being conducted by Fiocruz Ceará. The use of the tool will allow for decentralization across various laboratories, including the Lacen (Central Public Health Laboratories), and the performance of laboratory surveillance exercises, particularly inference assays for Sars-CoV-2 variants.

The first Omicron genomes in Brazil are from samples from the end of November, and by the end of December the variant was already the most frequent in the Southeast, Northeast, and South regions. Currently, Omicron is classified into four lineages (BA.1, BA.1.1, BA.2, and BA.3). In Brazil, up to the closing of the new edition of the Fiocruz Genomic Network Report, the lineages BA.1 (2.382 genomes), BA.1.1 (226 genomes), and BA.2 (1 genome) were identified.

inference tests

On the Fiocruz Genomics Network website RT-PCR inference data for variants performed by the Lacen (Central Public Health Laboratories) were included. A total of 3.984 tests have already been carried out in 16 states (Acre, Amazonas, Amapá, Roraima, Bahia, Ceará, Pará, Rio de Janeiro, Paraíba, Santa Catarina, Rio Grande do Norte, Rondônia, Rio Grande do Sul, Sergipe, São Paulo, and Tocantins) from November 2021 to January 2022. One of the assays for carrying out these tests, for the detection of SARS-CoV-2 and screening of variants, was developed by the Diagnostic Technology Laboratory of the Institute of Technology in Immunobiologicals (Bio-Manguinhos/Fiocruz) in partnership with the Respiratory Virus and Measles Laboratory of IOC/Fiocruz.

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