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. 2022 Oct 21;14(10):2314.
doi: 10.3390/v14102314.

Impact of Early Pandemic SARS-CoV-2 Lineages Replacement with the Variant of Concern P.1 (Gamma) in Western Bahia, Brazil

Josilene R Pinheiro  1   2 , Esther C Dos Reis  1 , Jéssica P Farias  1 , Mayanna M C Fogaça  1 , Patrícia de S da Silva  1   2 , Itana Vivian R Santana  1 , Ana Luiza S Rocha  1 , Paloma O Vidal  1 , Rafael da C Simões  1 , Wilson B Luiz  2 , Alexander Birbrair  3   4   5 , Renato S de Aguiar  6   7 , Renan P de Souza  6 , Vasco A de C Azevedo  6 , Gepoliano Chaves  8 , Aline Belmok  9 , Ricardo Durães-Carvalho  10   11 , Fernando L Melo  9 , Bergmann M Ribeiro  9 , Jaime Henrique Amorim  1   2
Affiliations

Impact of Early Pandemic SARS-CoV-2 Lineages Replacement with the Variant of Concern P.1 (Gamma) in Western Bahia, Brazil

Josilene R Pinheiro et al. Viruses. .

Abstract

Background: The correct understanding of the epidemiological dynamics of COVID-19, caused by the SARS-CoV-2, is essential for formulating public policies of disease containment.

Methods: In this study, we constructed a picture of the epidemiological dynamics of COVID-19 in a Brazilian population of almost 17000 patients in 15 months. We specifically studied the fluctuations of COVID-19 cases and deaths due to COVID-19 over time according to host gender, age, viral load, and genetic variants.

Results: As the main results, we observed that the numbers of COVID-19 cases and deaths due to COVID-19 fluctuated over time and that men were the most affected by deaths, as well as those of 60 or more years old. We also observed that individuals between 30- and 44-years old were the most affected by COVID-19 cases. In addition, the viral loads in the patients' nasopharynx were higher in the early symptomatic period. We found that early pandemic SARS-CoV-2 lineages were replaced by the variant of concern (VOC) P.1 (Gamma) in the second half of the study period, which led to a significant increase in the number of deaths.

Conclusions: The results presented in this study are helpful for future formulations of efficient public policies of COVID-19 containment.

Keywords: COVID-19; impact; variant of concern.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Fluctuations of COVID-19 cases and deaths due to COVID-19 during the period of study. (A) numbers of cases of COVID-19 per day during the period of study. (B) numbers of deaths due to COVID-19 per day during the period of study. Dots represent means. Horizontal bars represent medians.
Figure 2
Figure 2
Impact of COVID-19 according to gender or age. Comparisons of numbers of cases per day (A) and numbers of deaths per day (B) considering the whole period of study were carried out based on Student’s t-test. Significance was set as p ≤ 0.05. In addition, proportions of cases (C) and deaths (D) according to age groups were computed. Dots represent means. Horizontal bars represent medians.
Figure 3
Figure 3
Viral loads according to cycle threshold (CT) values. (A) fluctuation of viral loads found in samples collected from the study population along the period of study. (B) comparison of viral loads according to gender. (C) viral loads according to age group for each month of the study. (D) viral loads according to time (days) with symptoms, from November 2020 to July 2021. Dots represent means. Horizontal bars represent medians.
Figure 4
Figure 4
Substitution of SARS-CoV-2 lineages and its impact on local health. (A) Proportions of SARS-CoV-2 lineages found during the period of study. Viruses were classified based on genome sequencing and a specific RT-qPCR strategy capable of detecting specific mutations, as described in Section 2. EPLs, early pandemic lineages of SARS-CoV-2. (B) association between proportions of numbers of cases per month and numbers of deaths per month, as confirmed by linear regression analysis. (C) lack of association between proportions of viruses of the Gamma lineage found per month and proportions of cases per month (confirmed by linear regression analysis). (D) association between proportions of viruses of the Gamma lineage found per month and numbers of death per month (confirmed by linear regression analysis). Statistical significance was set as p ≤ 0.05.
Figure 5
Figure 5
Maximum-likelihood midpoint rooted phylogenetic tree based on 1117 (A) and 603 (B) representative genome sequences of SARS-CoV-2. Nextstrain’s subsampled SARS-CoV-2 genomic data from South America (including Brazil) since pandemic started up to August 2022 containing unfiltered (A) and filtered (B) sequences from the study. The SARS-CoV-2 genomes from this study are identified by the red circles. Tips are colored according to sampling locations. Yellow stars assume Shimodaira–Hasegawa (SH-like) test (A) and SH-aLTR/aBayes/ultrafast bootstrap support (B) based on 1000 replicates. Only values equal or greater than 75% are shown. Likelihood mapping of the final sequences alignment showing low phylogenetic noise, as required for reliable phylogeny inference (B). Abbreviations: VOC and VOI, Variant(s) of Concern and Variant(s) of Interest, respectively. EPLs, Early Pandemic Lineages. In letter B, “Brazil” represents whole-genome of SARS-CoV-2 Gamma variant from all Brazilian States and the Federal District. Branch lengths are drawn in scale of nucleotide substitutions per site according to the bar scale. Colors and symbols used in the panels are defined according to the legend to the left and right of the figure.
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