Primary health care and social isolation against COVID-19 in Northeastern Brazil: Ecological time-series study

Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak

BACKGROUND

We report a genomic surveillance of SARS-CoV-2 lineages circulating in Paraná, southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Paraná in March 2020 were the B.1.1.33 and B.1.1.28 variants. The variants B.1.1.28 and B.1.1.33 were predominant throughout 2020 until the introduction of the variant P.2 in August 2020 and a variant of concern (VOC), Gamma (P.1), in January 2021. The VOC Gamma, a ramification of the B.1.1.28 lineage first detected in Manaus (northern Brazil), has grown rapidly since December 2020 and was thought to be responsible for the deadly second wave of COVID-19 throughout Brazil.

METHODS

The 333 genomic sequences of SARS-CoV-2 from March 2020 to April 2021 were generated as part of the genomic surveillance carried out by Fiocruz in Brazil Genomahcov Fiocruz. SARS-CoV-2 sequencing was performed using representative samples from all geographic areas of Paraná. Phylogenetic analyses were performed using the 333 genomes also included other SARS-CoV-2 genomes from the state of Paraná and other states in Brazil that were deposited in the GISAID. In addition, the time-scaled phylogenetic tree was constructed with up to 3 random sequences of the Gamma variant from each state in Brazil in each month of 2021. In this analysis we also added the sequences identified as the B.1.1.28 lineage of the Amazonas state and and the Gamma-like-II (P.1-like-II) lineage identified in different regions of Brazil.

RESULTS

Phylogenetic analyses of the SARS-CoV-2 genomes that were previously classified as the VOC Gamma lineage by WHO/PANGO showed that some genomes from February to April 2021 branched in a monophyletic clade and that these samples grouped together with genomes recently described with the lineage Gamma-like-II. Additionally, a new mutation (E661D) in the spike (S) protein has been identified in nearly 10% of the genomes classified as the VOC Gamma from Paraná in March and April 2021.Finally, we analyzed the correlation between the lineage and the Gamma variant frequency, age group (patients younger or older than 60 years old) and the clinical data of 86 cases from the state of Paraná.

CONCLUSIONS

Our results provided a reliable picture of the evolution of the SARS-CoV-2 pandemic in the state of Paraná characterized by the dominance of the Gamma strain, as well as a high frequencies of the Gamma-like-II lineage and the S:E661D mutation. Epidemiological and genomic surveillance efforts should be continued to unveil the biological relevance of the novel mutations detected in the VOC Gamma in Paraná.

COVID-19 in Brazilian cities: Impact of social determinants, coverage and quality of primary health care

Background

Brazil, as many other countries, have been heavily affected by COVID-19. This study aimed to analyze the impact of Primary health care and the family health strategy (FHS) coverage, the scores of the National Program for Improving Primary Care Access and Quality (PMAQ), and socioeconomic and social indicators in the number of COVID-19 cases in Brazilian largest cities.

Methods

This is an ecological study, carried out through the analysis of secondary data on the population of all Brazilian main cities, based on the analysis of a 26-week epidemiological epidemic week series by COVID-19. Statistical analysis was performed using Generalized Linear Models with an Autoregressive work correlation matrix.

Results

It was shown that greater PHC coverage and greater FHS coverage together with an above average PMAQ score are associated with slower dissemination and lower burden of COVID-19.

Conclusion

It is evident that cities with less social inequality and restrictions of social protection combined with social development have a milder pandemic scenario. It is necessary to act quickly on these conditions for COVID-19 dissemination by timely actions with high capillarity. Expanding access to PHC and social support strategies for the vulnerable are essential.