Molecular testing and analysis of disease spreading during the emergence of COVID-19 in Macaé, the Brazilian National Capital of Oil

Abstract

The Brazilian strategy to overcome the spread of COVID-19 has been particularly criticized due to the lack of a national coordinating effort and an appropriate testing program. Here, a successful approach to control the spread of COVID-19 transmission is described by the engagement of public (university and governance) and private sectors (hospitals and oil companies) in Macaé, state of Rio de Janeiro, Brazil, a city known as the National Oil Capital. In 2020 between the 17th and 38th epidemiological week, over two percent of the 206,728 citizens were subjected to symptom analysis and RT-qPCR testing by the Federal University of Rio de Janeiro, with positive individuals being notified up to 48 h after swab collection. Geocodification and spatial cluster analysis were used to limit COVID-19 spreading in Macaé. Within the first semester after the outbreak of COVID-19 in Brazil, Macaé recorded 1.8% of fatalities associated with COVID-19 up to the 38th epidemiological week, which was at least five times lower than the state capital (10.6%). Overall, considering the successful experience of this joint effort of private and public engagement in Macaé, our data suggest that the development of a similar strategy countrywise could have contributed to a better control of the COVID-19 spread in Brazil. Quarantine decree by the local administration, comprehensive molecular testing coupled to scientific analysis of COVID-19 spreading, prevented the catastrophic consequences of the pandemic as seen in other populous cities within the state of Rio de Janeiro and elsewhere in Brazil.

Figure 1

Macaé, the National Oil Capital, occupying the lowest fatality rate due to COVID-19 among the 23 most populous municipalities (> 125,000 inhabitants) of the state of Rio de Janeiro, Brazil. South America Background from rnaturalearth package. Brazilian map, shape file from IBGE ftp://geoftp.ibge.gov.br/organizacao_do_territorio/malhas_territoriais/malhas_municipais/municipio_2019/Brasil/BR/br_unidades_da_federacao.zip. Rio de Janeiro map from IBGE, shape file . The figure was generated by the authors using the R 4.0.3 software and the packages rgdal, ggspatial and tidyverse available at ftp://geoftp.ibge.gov.br/organizacao_do_territorio/malhas_territoriais/malhas_municipais/municipio_2019/Ufs/RJ/rj_municipios.zip.

Figure 2

Relationship between the 4,611 COVID-19 RT-qPCR tests and positive result rates in Macaé, State of Rio de Janeiro, Brazil, between April 12th and September 12th, 2020. Note scale differences in (B) and (C). The diagonal in (E) represents a 1:10 ratio in absolute death and positive outcomes.

Figure 3

Distribution of the 815 positive tests for RT-qPCR COVID-19 by gender and days since the first symptom. This analysis is limited to patients from the municipal Coronavirus Screening Center for COVID-19 (CSC), Macaé, state of Rio de Janeiro, Brazil, between April 12th and September 12th, 2020. 155 cases were excluded from the analysis, since the day of the first symptom was not available.

Figure 4

Prevalence of symptoms reported by 878 patients that tested positive for COVID-19 in CSC and the hospital settings of Macaé, state of Rio de Janeiro, Brazil, between April 12th and 12th September 2020. Number of positive tests are in brackets.

Figure 5

Ordination of women (A) and men (B) positively tested for COVID-19 in the municipal Coronavirus Screening Center for COVID-19 (CSC) on a multidimensional space formed by the two axes of the NMDS. Mean scores (± standard error) between gender and age class in C.

Figure 6

∆Ct of SARS-CoV-2 positive patients with mild and severe symptoms of COVID-19. Patient RT-qPCR results were separated in four different groups based on days after the first symptoms and severity of the disease. Mild < 5 are ∆Ct values from 257 patients with mild COVID-19 symptoms tested until 5 days from the first symptoms (89% of them from the municipal Coronavirus Screening Center for COVID-19 patients-CTC), Severe < 5 are 20 patients hospitalized (80% of them) early after infection, or non-hospitalized patients with severity-related symptoms or still COVID-19 associated fatalities. The same classification was adopted for the patients with more than 5 days of symptoms:158 Mild > 5 (85% of them from the CTC) and 32 Severe > 5 (78% of them from hospitals). Significant differences among groups are represented by different letters above boxplots.

Figure 7

Spatial distribution of accumulated RT-qPCR positive cases and deaths in Macaé, Rio de Janeiro. (A,B) Map representation of the different neighborhoods of Macáe, RJ and SSR representation of RT-qPCR positivity (A) and deaths (B). (C,D) The exact locations of each occurrence (case and death) and the density level curves with 25, 50 and 75% of the estimated cases using the Kernel smoothing method. Background from mapmisc package. Macaé map from GeoMacaé, shape file available at http://www.macae.rj.gov.br/midia/conteudo/arquivos/1452711889.zip. The figure was generated using the R 4.0.3 software and the packages rgdal, tmap, adehabitatHR and tidyverse.

Figure 8

Number and percentage of positive individuals among the 4,639 tests for COVID-19 RT-qPCR in Macaé, State of Rio de Janeiro, Brazil, according gender (Men = 1986; Women = 2653), between April 12th and September 12th, 2020. Numbers above columns refer to the percentage of positive results within each gender and age class. See Table 3 to identify age classes with significant differences between gender (in bold).