Laboratory infrastructure in the state of São Paulo forms COVID-19 diagnostic testing platform

The initiative is coordinated by Butantan Institute and includes units in several cities accredited by Adolfo Lutz Institute (IAL), the regional reference laboratory. Short supply is the main bottleneck delaying the expansion of testing in the state.

By André Julião and Maria Fernanda Ziegler  |  Agência FAPESP – A platform comprising some 20 laboratories, mostly public-sector and linked to universities or research institutions in the state of São Paulo, Brazil, is being built to optimize diagnostic testing for COVID-19. The initiative is coordinated by Dimas Covas, the director of Butantan Institute and a member of the São Paulo State Coronavirus Contingency Center. One of its remits is obtaining supplies for test kits to detect the novel coronavirus, SARS-CoV-2.

“Reagents are being bought and this month [April] we’ll take delivery of the first batch of diagnostic test kits ordered from South Korea. It’s all coming together,” Covas told Agência FAPESP. 

Covas is also principal investigator for the Center for Cell-Based Therapy (CTC), one of the Research, Innovation and Dissemination Centers (RIDCs) funded by FAPESP.

The platform is spearheaded by the Adolfo Lutz Institute (IAL), the macroregional reference laboratory accredited by the Brazilian Ministry of Health. It also includes Butantan Institute and several private laboratories, as well as task forces established by all three state universities in São Paulo to deploy facilities, equipment and personnel in this mission.

The platform was officialized on April 2, with the announcement that six of its laboratories have been accredited for testing purposes by IAL. Its initial lineup also included the hospitals run by the University of São Paulo’s Medical School (HC-FM-USP) and Ribeirão Preto Medical School (FMRP-USP), as well as the latter’s Blood Center; the Clinical Pathology Laboratory attached to the University of Campinas’s hospital (LPC-HC-UNICAMP); and the Blood Center at the hospital run by São Paulo State University’s Botucatu Medical School (HC-FMB-UNESP).

The Adolfo Lutz Institute is expected to conclude the certification of a total of 45 laboratories by the end of April. Institutions such as the Genomic Research Laboratory in the Biology Department of UNESP’s Institute of Biosciences, Letters and Exact Sciences (IBILCE) in São José do Rio Preto, and USP’s School of Animal Science and Food Engineering (FZEA) in Pirassununga are currently being accredited by IAL. 

Short supply

The platform will help surmount the main challenge faced by laboratories, which is a shortage of reagents and other materials required for diagnostic testing.

“The goal is to centralize procurement of these supplies by the São Paulo State Department of Health. At this time it’s particularly important to source inputs from trustworthy suppliers,” said Roger Chammas, Vice Director of FM-USP and coordinator of the diagnosis network set up by his university (Rede USP para o Diagnóstico da COVID-19, RUDIC), which is expected to perform 1,500 tests per day.

According to Chammas, also a participant in cancer research projects with FAPESP’s support, FM-USP has a stock of diagnostic tests but the number falls short of current needs. The difficulty of obtaining reagents and other supplies, he explained, is due to the fact that most are imported and global demand is huge at the moment because of the pandemic.

“Our dependence on imports is enormous,” he said. “Brazil has very few producers of reagents. The main producers are overseas and also few in number, so there’s little scope for negotiation. Countries like South Korea or China with highly developed industrial complexes are able to organize and produce diagnostic test kits themselves.”

Molecular tests

UNICAMP has built infrastructure and trained personnel to perform 40,000 tests. Supplies for the first 6,000 are set to arrive soon. More inputs have been ordered for another 30,000 but may never arrive.

“The US has banned shipments to other countries so we’re forced to look for other solutions,” said Alessandro dos Santos Farias, a professor in UNICAMP’s Biology Institute and responsible with others for winning testing certification for the university hospital’s Clinical Pathology Laboratory (read more at: agencia.fapesp.br/32998).

Farias and other researchers at UNICAMP aim to validate reagents (used to extract RNA from samples), enzymes and probes for PCR testing. PCR stands for polymerase chain reaction and is the screening assay method recommended by the World Health Organization.

“We’ve established a standard for certain inputs and based on this we’re testing other brands to see if the results are the same. With this validation we won’t be dependent on only a few suppliers,” said Farias, who is also testing products made in Brazil.

All validated protocols will be posted on the task force’s website to help other laboratories avoid stoppages for lack of supplies.

Laboratory structure

UNESP’s Botucatu Blood Center is ready to begin doing 150 tests per day. “Some labs including Botucatu already work on a routine basis with the Health Ministry, doing tests for HIV and hepatitis B and C. We’ll use these routines to do tests for COVID-19,” said Rejane Grotto, a professor in UNESP’s School of Agronomic Sciences and the scientist in charge of the testing program.

UNESP’s network also includes the Clinical Immunology and Molecular Biology Laboratories in Araraquara, and the Genomic Research Laboratory in São José do Rio Preto, which is awaiting accreditation by IAL.

“These labs were set up in the 2000s for the FAPESP-funded research project Viral Genetic Diversity Network (VGDN), whose main aim even back then was to establish a network of labs equipped to study the genetic diversity of viruses and contribute in situations like the pandemic we’re now facing by providing a rapid response in terms of public health,” Grotto explained.

The project enabled the construction of the BSL-3 facility in Araraquara and BSL-2 facilities in Botucatu and São José do Rio Preto, sufficient for PCR and similar tests that manipulate viral genetic material to identify SARS-CoV-2 (the highest level of biosafety is BSL-4). 

Organization of the network of reference laboratories to test for COVID-19 is the first initiative of the scientific steering committee set up by UNESP for action regarding the pandemic. “The network will provide testing in short order. This is the main bottleneck in Brazil at the moment. The fact that UNESP has several campuses across the state makes the initiative even more strategic by assuring wide coverage and contributing to epidemiological surveillance of the pandemic,” Grotto said.

The testing network will help manage the spread of the disease in the interior of the state and orient containment actions. “If we can diagnose faster we’ll also be able to test people who’ve been in contact with those infected and try to contain transmission by this means,” Grotto said. “This was done in Singapore and South Korea, countries considered successful in their response to the coronavirus pandemic. They did some 10,000 tests per day.”

The network will also conduct research in an integrated manner. “We plan to work on two fronts, diagnosis and research,” Grotto said. “We’ll do research on epidemiological aspects, interaction between cells and the virus, development of new technology, and tools to predict outcomes and probable complications, for example. It’s important to investigate the effects of this syndrome now, since the research is translational. The results can help save lives.”