New virus variants are now dominant in Amazonas and six other Brazilian states – Fiocruz

RIO DE JANEIRO, BRAZIL – The coronavirus variants with higher transmission potential and possibly more lethal is now dominant in six Brazilian states, in addition to Amazonas, according to a study by Fiocruz (Oswaldo Cruz Foundation).

The study analyzed approximately 1,000 samples of the virus collected in 8 Brazilian states in the Northeast, South and Southeast regions: Alagoas, Ceará, Minas Gerais, Paraná, Pernambuco, Rio de Janeiro, Rio Grande do Sul and Santa Catarina.

Of the 8 states analyzed, 6 showed the presence of the variant as dominant, i.e., with prevalence higher than 50% of the analyzed samples: Ceará (71.1%), Paraná (70.4%), Pernambuco (50.8%), Rio de Janeiro (62.7%), Rio Grande do Sul (62.5%) and Santa Catarina (63.7%). Only 2 of the analyzed states did not show the variant’s predominant presence: Alagoas (42.6%) and Minas Gerais (30.3%).

Ex-Minister of Health Luiz Henrique Mandetta predicted on January 27th, that within 60 days Brazil may experience a mega-epidemic caused by the new variant of the coronavirus, detected in Manaus. According to him, the transfer of patients from Amazonas to other states may increase the spread of this new strain.

The study identifies the presence of one of the three variants of concern (called VOCs) of Sars-CoV-2, the British (B.1.1.7), the South African (B.1.351), and the Brazilian or Manaus (P.1), which have spread worldwide and cause concern because they are more transmissible and, in the case of the South African and Amazonas strains, reduce the action of antibodies that ensure immune protection.

However, the tests performed are unable to distinguish between the 3 variants, i.e., the prevalence reported may refer to any of the three – or even to a set of them.

Unlike the genome sequencing method, which searches for new variants of the existing virus and those not yet known, the Fiocruz study used RT-PCR tests, similar to the ones used for the diagnosis of patients infected with the virus, to detect the variants of concern.

The new feature compared to the common test is the search tool for a part of the gene that encodes the virus’ Spike S protein (used as a gateway to infect cells) that presents a deletion in the 3 variants – that is, it does not exist in the variant.

If the test “lights up” for that region, researchers can rule out that sample as being from an ancestral strain of the virus, which does not carry the deletion.

The customized test was designed by researcher Felipe Naveca, in the Amazon Fiocruz, who analyzed 500 samples collected in the Amazonas state region in January and found the prevalence of P.1 in 71% of them.

In an exercise of exclusion, as there are no proven reports of the presence of the South African variant in the country, and the incidence of the UK variant is not as significant, it is more likely that the rates found refer to the distribution of the P.1 variant, since the laboratory network linked to the Ministry of Health has already detected the variant in 17 Brazilian states.

In the Fiocruz technical note, prepared by the foundation’s Covid-19 Observatory, researchers point out that “the new protocol does not replace the need for monitoring through genetic sequencing, but rather complements it, offering a quick picture of the variants’ circulation for decision making in the fight against the pandemic.”

“Brazil is currently experiencing its worst moment of the pandemic, with a high incidence of cases and consecutive records in the rolling average of deaths.”

According to experts, the surge in the number of cases and deaths in the country is directly related to the increasingly rapid spread of P.1 in the country.

Fiocruz was not the only one to detect the presence of virus variants through RT-PCR exams. Dasa laboratory, a Brazilian leader in diagnostic medicine, which first identified the UK variant in the country, has also been using a specific protocol to detect the new strains of Sars-CoV-2 in circulation.

Created in partnership with researchers from the Institute of Tropical Medicine at USP (IMT/USP), the test is able to make an initial separation of all virus samples whose origin is the ancestral lineage or the UK one, and then, with a new analysis, confirm if it is really the P.1.

In a study with 91 samples collected in Greater São Paulo, the new test found a 77% incidence of this high transmissible lineage in the region. According to José Eduardo Levi, research and development coordinator at Dasa and researcher at IMT/USP, the stronger the presence of a variant in a sample set, the higher the prevalence of this strain among the population.

“If today we are talking about an 80%, 90% prevalence of P.1, testing 100 to 200 samples that are representative of the universe [of cases] is enough to verify this more dominant presence,” he says.

Camila Romano, researcher at USP’s Clínicas Hospital and IMT/USP, an iconic case is the recent collapse in Araraquara, São Paulo. “In mid-January to early February, I analyzed some samples coming from there that showed an 84% incidence of the P.1. Since February 18th, all samples I sequenced from Araraquara were P.1.”

The biologist created a protocol similar to the one developed by Fiocruz, but with an advantage: the test is able to detect infection at the same time from two different coronavirus strains. “Today we have several strains circulating at the same time in the country and, what is worse, with a chance of infection by more than one strain,” she says.

The chance of reinfection associated with this strain also impacts the health system, which is burdened with more patients in need of hospital care. According to the researcher, in all areas currently in collapse, if there is testing, the P.1 will be detected.

Because it is faster and less expensive than sequencing, the test developed by Romano has also been used in other research laboratories that aim to monitor the circulation of the virus in the country, including Dasa.

However, the main obstacle is the importation of supplies and reagents, particularly in the public health system. Romano says that they used supplies from the UK cooperation group and, at the same time, made a request to import reagents. “We have already used all the reagents from the UK and the order we placed in the country hasn’t even arrived yet,” he says.

In addition to the problems in importing supplies, the lack of research resources also hinders virus evolution studies and genetic sequencing. As a result, the time spent is much longer, in addition to the equipment used being expensive, negatively impacting the genomic surveillance in the country.

Biomedical expert Raphael Parmigiani explains that if there were more resources in the country, the ideal would be to conduct a more aggressive genetic sequencing of the samples. In their absence, the use of real-time PCR tests to search for variants is a solution.

“The strategy we can employ in the country is a combination of the two technologies: to sequence as many as possible with the resources we have available, and to determine the distribution of the already known strains, use the PCR test adapted to detect these strains, which any molecular biology laboratory in the country is able to do,” says Parmigiani.