Abstract:The SARS-CoV-2 P.1 lineage is associated with increased transmissibility and/or immune evasion and presents a dynamic evolution in Brazil. The significance of our research relies in the fact that we evaluated the SARS-CoV-2 lineages circulating in Southern Brazil between March 2020 and May 2021.
“…Among several lineages, along these two years of pandemic, various Variants of Concern (VOCs), such as Alpha, Beta, Gamma, Delta, and Omicron, carrying signature aminoacid substitutions (especially in the spike protein) circulated in RS state (Gularte et al, 2022; Wink et al, 2022; Gräf et al, 2022). The sublineage P.1.2, a Gamma-like variant also considered as a Variant of Interest, was initially identified in RS state (Franceschi et al, 2021), despite other studies estimating its divergence between late 2020 and early 2021 in São Paulo state (Junior et al, 2021).…”
The SARS-CoV-2 is the virus responsible for the COVID-19 pandemic and is plaguing the world since the end of 2019. Different lineages have been discovered ever since and the Gamma lineage, which started the second wave of infections, was first described in Brazil, one of the most affected countries by pandemic. Describing the viral genome and how the virus behaves is essential to contain its propagation and to the development of medications and vaccines. Therefore, this study analyzed SARS-CoV-2 sequenced genomes from Esteio city in Rio Grande do Sul, Southern Brazil. We also comparatively analyzed genomes of the two first years of the pandemic from Rio Grande do Sul state for understanding their genomic and evolutionary patterns. The phylogenomic analysis showed monophyletic groups for Alpha, Gamma, Delta and Omicron, as well as for other circulating lineages in the state. Molecular evolutionary analysis identified several sites under adaptive selection in membrane and nucleocapsid proteins which could be related to a prevalent stabilizing effect on membrane protein structure, as well as majoritarily destabilizing effects on C-terminal nucleocapsid domain.
“…Among several lineages, along these two years of pandemic, various Variants of Concern (VOCs), such as Alpha, Beta, Gamma, Delta, and Omicron, carrying signature aminoacid substitutions (especially in the spike protein) circulated in RS state (Gularte et al, 2022; Wink et al, 2022; Gräf et al, 2022). The sublineage P.1.2, a Gamma-like variant also considered as a Variant of Interest, was initially identified in RS state (Franceschi et al, 2021), despite other studies estimating its divergence between late 2020 and early 2021 in São Paulo state (Junior et al, 2021).…”
The SARS-CoV-2 is the virus responsible for the COVID-19 pandemic and is plaguing the world since the end of 2019. Different lineages have been discovered ever since and the Gamma lineage, which started the second wave of infections, was first described in Brazil, one of the most affected countries by pandemic. Describing the viral genome and how the virus behaves is essential to contain its propagation and to the development of medications and vaccines. Therefore, this study analyzed SARS-CoV-2 sequenced genomes from Esteio city in Rio Grande do Sul, Southern Brazil. We also comparatively analyzed genomes of the two first years of the pandemic from Rio Grande do Sul state for understanding their genomic and evolutionary patterns. The phylogenomic analysis showed monophyletic groups for Alpha, Gamma, Delta and Omicron, as well as for other circulating lineages in the state. Molecular evolutionary analysis identified several sites under adaptive selection in membrane and nucleocapsid proteins which could be related to a prevalent stabilizing effect on membrane protein structure, as well as majoritarily destabilizing effects on C-terminal nucleocapsid domain.
“…The samples submitted by LACEN-RS for genetic characterization were representative of the SARS-CoV-2 scenario in RS, as the proportion of lineages was similar to that of all RS samples submitted to GISAID ( Supplementary Table 3 ). As observed in RS and the rest of the country, with the emergence of B.1.1.28, B.1.1.33, and P.2, the number of cases increased due to the high transmissibility of these variants 49 - 53 . Using this collection, we found no association between the most frequent variants and any specific demographic data.…”
Background:
Brazil has one of the highest numbers of COVID-19 cases and deaths. Rio Grande do Sul (RS) in southern Brazil is one of the leading states in terms of case numbers. As part of the national public health network, the State Central Laboratory (LACEN-RS) changed its routine in 2020 to focus on the diagnosis of COVID-19. This study evaluated the laboratory surveillance of COVID-19 suspected cases analyzed at the LACEN-RS in 2020.
Methods:
Viral detection was performed using RT-qPCR in samples from patients with respiratory infection who met the study criteria. Viral RNA was isolated using commercial manual kits or automated extractors, and SARS-CoV-2 RT-qPCR was performed using the Bio-Manguinhos/Rio de Janeiro, IBMP/Paraná, or Allplex 2019-nCoV assay. In total, 360 representative SARS-CoV-2 samples were sequenced using the Illumina platform.
Results:
In total, 31,197 of 107,578 (positivity rate = 29%) tested positive for SARS-CoV-2. The number of RT-qPCR tests performed per month followed the COVID-19 epidemic curve observed for the state, with peaks in July-August and December. Females accounted for 63% of the samples, whereas the positivity rate was higher among males (33.1% males vs. 26.5% females). The positivity rate was higher in adults aged 50-79 years compared to the overall positivity rate. The majority of cases were observed in the capital, Porto Alegre, and the metropolitan region. Ten distinct lineages were identified, with B.1.1.28, B.1.1.33, and P.2 being the most frequent.
Conclusions:
Here, we describe laboratory surveillance of COVID-19 to identify priorities for epidemiological surveillance actions in RS.
“…2 . Notably, the country that first detected a variant that could differ from the origin country of the variant, such as the P.1 Gamma variant, which was first detected in travelers returning from Brazil to Japan 30 , 31 . Figure 2 Potentially consequential SARS-CoV-2 variant lineages first detected in each country.…”
The coronavirus disease 2019 (COVID-19) pandemic has been facilitated by the intermittent emergence of consequential variant strains. This study evaluated the geographic disproportionality in the detection of consequential variant lineages across countries. As of November 2021, a total of 40 potentially consequential SARS-CoV-2 variant lineages have been identified. One-hundred repeated simulations that randomly produced consequential variants from overall COVID-19 cases worldwide were performed to evaluate the presence of geographical disproportion in the occurrence of consequential variant outbreaks. Both the total number of reported COVID-19 cases and the number of reported genome sequences in each country showed weak positive correlations with the number of detected consequential lineages in each country. The simulations suggest the presence of geographical disproportion in the occurrence of consequential variant outbreaks. Based on the random occurrence of consequential variants among COVID-19 cases, identified consequential variants occurred more often than expected in the United Kingdom and Africa, whereas they occurred less in other European countries and the Middle East. Simulations of the occurrence of consequential variants by assuming a random occurrence among all COVID-19 cases suggested the presence of biogeographic disproportion. Further studies enrolling unevaluated crucial biogeographical factors are needed to determine the factors underlying the suggested disproportionality.
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