By correlating genomic sequencing data and epidemiological analyzes in the city of São José do Rio Preto (SP), researchers were able to demonstrate the impact of the prevalence of the P.1 variant (now called Gamma) in the discharge of cases and deaths from covid-19. The greater transmissibility of this strain was associated with a significant increase in severe cases (127%) and deaths (162%) in March and April 2021, in the municipality of the interior of São Paulo.
The study, released on the medRxiv platform yet without peer review, highlights the importance of vaccination to protect the population and the effectiveness of the 15-day lockdown, stipulated in the city in March, to contain the spread of the virus.
“These are expected conclusions, but they need clear proof because of the environment in which we live. Our study confirms that vaccines protect against death from covid-19 and lockdown works to reduce the circulation of the virus. Other than that, we were able to demonstrate that P1 is, in fact, a more aggressive variant, something that was not yet so clear among the scientific community”, says Maurício Lacerda Nogueira, professor at the São José do Rio Preto Medical School (Famerp) .
The study was carried out by Famerp’s Virology Research Laboratory at the Hospital de Base (HB) in Rio Preto, in partnership with the São Paulo State University (Unesp), University of São Paulo (USP), Bill & Melinda Gates Foundation, University of Washington , University of Texas Medical Branch and Municipal Health Secretariat of São José do Rio Preto. The group was supported by FAPESP (Foundation for Research Support of the State of São Paulo), by the Corona-ômica Network (maintained by the Ministry of Science, Technology and Innovation through the Financier of Studies and Projects and the National Council for Scientific and Development). Technological), from the Butantan Institute and the National Institutes of Health, in the United States.
As part of the study, genomic surveillance of SARS-CoV-2 in Rio Preto and region has been carried out since October 2020. The researchers analyzed 272 complete genomes of the new coronavirus in order to detect the prevalence of the variants. Of the 12 strains identified, the most prevalent were P.1 (72.4%), P.2 (11%), B.1.1.28 (5.6%) and N.9 (4.6%).
the ball of variants
Variants are mutated forms of the virus and, although the vast majority present epidemiological behavior similar to that of the ancestral strain, some of them are of concern because they are potentially more transmissible or even more lethal. The P.1 (Gama) lineage appeared in early November 2020, in Manaus (AM), and quickly spread to other Brazilian states, mainly those in the Southeast region.
In December 2020, the B.1.1.7 (Alpha) variant was first detected in the UK. It is attributed to an increased transmission between 30% and 50% and the severity of cases is 30% higher.
In South Africa, the B.1.351 (Beta) variant was detected for the first time, associated with an increased risk of transmission and a reduction in viral neutralization by therapy with monoclonal antibodies, convalescent sera and post-vaccination sera.
More recently, the Delta variant, first detected in India, has spread around the world, possibly impacting the recent rise in cases in Europe, the United States and China.
Gamma variant, a case study
Nogueira explains that, starting at the end of last year, the city of São José do Rio Preto has experienced two major peaks in cases and deaths: one in December 2020 and another in February 2021, when the occurrences of the disease exploded.
“According to the analysis, in October of last year several variants of the coronavirus were circulating. In December, however, there was a predominance of P2 [detectada pela primeira vez no Rio de Janeiro], which may have resulted in the discharge of cases, but without an increase in the severity of the disease. It was on January 26, 2021 that we detected the first case of P1 in the city and, soon after, this strain became dominant. It is during this period, starting in March, that there is an increase of more than 100% in the number of serious cases and deaths”, reveals Nogueira.
The researcher explains that it is not possible to say that P2 was responsible for the increase in cases at the end of 2020. This is because the holiday period also coincided with a greater movement of people throughout the country and, consequently, greater transmission of the disease .
In the case of P1 (Gama), according to the researcher, this correlation can be proven, which puts an end to a great discussion in the scientific community to find out whether the variant was really more aggressive and responsible for a greater number of deaths.
“Studies carried out in Manaus indicated the death of a very high number of people and, in January, the total collapse of the health system in Amazonas occurred, oxygen was lacking, people died without being able to breathe and even babies in incubators [que não necessariamente tinham covid-19] they needed to be transferred to receive treatment in other states. In addition to the variant, there were a number of other well-known factors that led to a situation of humanitarian crisis”, he says.
The situation in São José do Rio Preto in March was different from Manaus in January 2021. The municipality of São Paulo, with 400 thousand inhabitants, has a more robust health system and adopted a lockdown at the peak of transmission of the P1 variant. “In Rio Preto there was no collapse of the health system, nor was there a lack of oxygen. What happened was very hard, we got to have 300 people in ICUs [unidades de terapia intensiva], but without reaching the maximum capacity. We had a day or two with 100% bed occupancy. Even with this better scenario, mortality was much higher than at previous peaks. This was because the P1 is a more aggressive variant”, he assesses.
Vaccines save lives
Another important factor was that the period of discharge of P1 infections in the city of São Paulo coincided with the vaccination of the elderly. “When there was the spread of P1 in the city, almost 100% of those over 70 years of age were vaccinated, most with CoronaVac. According to the study, vaccines correspond to between 60% and 70% of protection against death in severe cases in this vaccinated population, which is great news”, he says.
According to Nogueira, genomic surveillance studies are continuing. The team will both investigate what happened last year (before the new variants appeared) and monitor the coming months of the pandemic. “We continue to do these analyzes and correlations on a weekly basis. We have not yet detected the Delta variant in the county, but I believe this is just a matter of time. The study will allow us to monitor the impact of the likely competition between Delta and Gamma”, he predicts.
He points out that, although there was an occurrence of the Gamma variant in England and the United States, Europe was not affected by it. “There, Gama did not directly compete with Delta. But this could be happening here in Brazil, as shown by studies in Rio de Janeiro, where the prevalence of Delta is advancing”, he says.
The article Effects of SARS-CoV-2 P.1 introduction and the impact of covid-19 vaccination on the epidemiological landscape of São José Do Rio Preto, Brazil can be read in www.medrxiv.org/content/10.1101/2021.07.28.21261228v1.