Project creates system to track circulation of variants of SARS-CoV-2 in the city of São Paulo

The initiative is being implemented as a partnership between local government, DASA Laboratories and FAPESP.

By Karina Toledo  |  Agência FAPESP – A partnership between local government, FAPESP, and DASA S.A., a clinical diagnostics company, is implementing a system that tracks the circulation of variants of the novel coronavirus in the city of São Paulo (Brazil).

The goal is to analyze 384 nasopharyngeal swabs per week from inhabitants of all parts of the city who attend public health clinics and test positive for SARS-CoV-2. The University of São Paulo’s Institute of Tropical Medicine (IMT-USP) will submit the material to RT-PCR testing to detect the presence of five variants of concern: Alpha (B.1.1.7, first identified in the UK), Beta (B.1.351, South Africa), Delta (B.1.617, India), Gama (P.1, Manaus in the Brazilian Amazon), and Zeta (P.2, Rio de Janeiro). If the result is negative for all five, the sample will be sequenced to identify the lineage. In addition, 25% of the samples processed by RT-PCR testing will be selected at random each month for whole-genome sequencing by DASA’s team.

“We’ve already received samples collected at the end of May and start of June, and analysis has begun. We also mean to study retrospectively material collected since January 2021. One of the aims is to try to find out when and where the Gama variant entered São Paulo, and how it spread. Another is to see if the Delta variant is now circulating here,”* said Ester Sabino, a professor at IMT-USP and co-principal investigator for the study alongside Carlos Fortaleza, a professor at São Paulo State University (UNESP) in Botucatu.

Samples will be selected for analysis in proportion to the population of each region of the city (north, south, east, west, center and southeast), avoiding severity bias. The municipal government will supply the researchers with certain kinds of patient data, such as sex, age, and place of residence, as well as whether they had been vaccinated, the date on which the swab was taken, and the date of symptom onset.

“Because we’re working with data from samples, they must be representative of the population as a whole and well distributed in time and space. In other words, the data must be a maquette of what’s happening in the city. We want to be able to look at this perfect miniature and see how the variants are distributed at the moment,” said Fortaleza, who designed the project.

The group used statistical techniques based on the size of the city’s population, and assuming a 5% margin of error, to arrive at 384 as the number of weekly samples needed to map the circulation of variants whose presence could not be quantified in advance. 

According to Fortaleza, the purpose of the project is to implement a genomic surveillance and epidemiological control system that is sensitive enough not to allow any variant in circulation to go unnoticed, representative in the sense that variants are detected in proportion to their actual distribution, agile enough to produce data in time for control measures to be taken, and adaptable to changing conditions.

The initiative was taken by city hall and “catalyzed” by FAPESP, according to Luiz Eugênio Mello, its Scientific Director. “We want to convert what should be a routine activity for local government into a project conducted along lines we can support,” he said. “The project involves an important persuasive element, and we want it to suggest novel organizational setups in which academia, government and private enterprise can interact quickly and effectively.”

Benefits

For José Eduardo Levi, a researcher at IMT-USP and DASA, genomic surveillance is one of the main pillars of the effort to combat COVID-19, alongside vaccination, testing and social distancing.

“The virus is evolving right in front of our eyes, and this strategy will let us find out quickly if any variants are likely to produce a fresh wave so we can intervene as soon as possible,” he said.

Based on genome sequencing, it is possible to infer whether a new strain can be considered a variant of concern (VOC). “If a cluster of samples that suggest concern is detected in a given neighborhood, for example, the authorities can distribute masks and reinforce social distancing and vaccination in a targeted manner,” Levi said. “Or if severe cases in vaccinated individuals are observed in an area, the immunization campaign can switch to a different vaccine there.”

According to Sabino, the analyses conducted as part of the project will help scientists understand how novel variants spread in São Paulo and identify viral dissemination hubs that can be targeted by official intervention. 

“FAPESP’s drive to contribute to public policy, as it’s been doing for years via programs such as PPSUS [Research Program for SUS, the national health system], represents a very important commitment to science for the benefit of life,” Fortaleza said. “Combining knowledge in epidemiology, virology and molecular biology with the practical work done by City Hall’s technicians builds bridges, as a basis for the emergence of things that are very important for public health.”

* Note: On July 7, the São Paulo State Government confirmed community transmission of SARS-CoV-2’s Delta variant in the city of São Paulo, two days after a Delta variant case turned public: A 45-year old man who works in home office and has not had any recent contact with people traveling abroad.