Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation

Demoliner, Meriane; Silva, Mariana Soares da; Gularte, Juliana Schons; Hansen, Alana Witt; Almeida, Paula Rodrigues de; Weber, Matheus Nunes; Heldt, Fágner Henrique; Silveira, Frank Ferreira; Filippi, Micheli; Pereira, Vyctoria Malayhka de Abreu Góes; Silva, Francini Pereira da; Mallmann, Larissa; Fink, Pietra; Valim, Andréia Rosane de Moura; Possuelo, Lia Gonçalves; Fleck, Juliane Deise; Spilki, Fernando Rosado

doi:10.1016/j.meegid.2021.105134

Cited by 11 publications

(9 citation statements)

References 18 publications

(20 reference statements)

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“…COVID-19 epidemic in Brazil, during 2021, was driven by the spread and predominance of the VOC Gamma (lineage P.1) which caused the highest wave of SARS-CoV-2, considering the number of cases, deaths, and hospitalization per day ( Demoliner et al, 2021 ). The first Delta variant local case described in Brazil was in July 2021, by Lamarca et al, (2021) .…”

Section: Discussionmentioning

confidence: 99%

“…Since the Delta lineage started to appear in RS State, the cases increase monthly as observed in our results. Despite this, in contrast to the huge COVID-19 epidemic wave associated with the substitution of B.1.1.28 by the VOC Gamma ( Demoliner et al, 2021 ; Faria et al, 2021 ), Delta viral lineage replacement occurred without the SARS-CoV-2 cases increase, probably due to the high immunity levels (natural and/or vaccinated) in the RS State population ( Secretaria da Saúde do Rio Grande do Sul, 2021b ). This scenario is similar to what has happened in the European Union (EU) since its emergence in March 2021.…”

Section: Discussionmentioning

confidence: 99%

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Early introduction, dispersal and evolution of Delta SARS-CoV-2 in Southern Brazil, late predominance of AY.99.2 and AY.101 related lineages

et al. 2022

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The emergence of Variants of Concern (VOC) presenting an unusual number of new mutations is one of the most remarkable features of SARS-CoV-2. The Delta variant, since its appearance, replaced the VOC Gamma, which was responsible for the major COVID-19 wave in Brazil. In this study, we performed a Delta whole-genome sequencing of 183 samples as part of a major genomic surveillance study performed since the beginning of the pandemic. Here, we showed an emergence, widespread dispersion and consolidation of the Delta variant in Rio Grande do Sul State, completely replacing the Gamma variant in a four to five months period. Performing the phylogenetic and phylodynamic analysis, the majority of the sequences generated herein were classified as AY.99.2, AY.99.2-like and AY.101. AY.99.2 Delta-related lineage has been widely reported in Brazil and in the Americas as well. Altogether, our findings provided a mutational profile of the sequences and presented high substitutions per site in the root-to-tip phylogenetic tree, corroborating studies that show the high mutational rate of SARS-CoV-2 over time.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Early introduction, dispersal and evolution of Delta SARS-CoV-2 in Southern Brazil, late predominance of AY.99.2 and AY.101 related lineages

et al. 2022

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“…Using molecular clock phylogenetics, it was estimated that the Gamma variant appeared in November 2020 in Manaus, which was experiencing the lowest levels of daily new confirmed cases since the beginning of the pandemic [ 77 ]. The emergence of the Gamma variant explains the increase of cases in the region [ 78 ]. The wide propagation of this variant was also linked to a decrease in preventive measures which were dependent on the decisions of each state and municipality.…”

Section: Herd Immunity and Variantsmentioning

confidence: 99%

COVID‐19 in Latin America and the Caribbean: Two years of the pandemic

et al. 2022

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Worldwide, nations have struggled during the coronavirus disease 2019 (COVID‐19) pandemic. However, Latin America and the Caribbean faced an unmatched catastrophic toll. As of March 2022, the region has reported approximately 15% of cases and 28% of deaths worldwide. Considering the relatively late arrival of SARS‐CoV‐2, several factors in the region were determinants of the humanitarian crisis that ensued. Pandemic unpreparedness, fragile healthcare systems, forthright inequalities, and poor governmental support facilitated the spread of the virus throughout the region. Moreover, reliance on repurposed and ineffective drugs such as hydroxychloroquine and ivermectin—to treat or prevent COVID‐19—was publicised through misinformation and created a false sense of security and poor adherence to social distancing measures. While there were hopes that herd immunity could be achieved after the region's disastrous first peak, the emergence of the Gamma, Lambda, and Mu variants made this unattainable. This review explores how Latin America and the Caribbean fared during the first 2 years of the pandemic, and how, despite all the challenges, the region became a global leader in COVID‐19 vaccination, with 63% of its population fully vaccinated.

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“…This lineage was responsible for many positive cases and hospitalizations, as well as a large number of deaths. 15 Besides, cases of more extended infection periods than usual were reported. These persistent infections may play a significant role in transmission rates and in the possibility of new mutations in the SARS-CoV-2 genome, which may cause new variants to appear.…”

Section: Discussionmentioning

confidence: 99%

Prolonged SARS-CoV-2 Infection and Intra-Patient Viral Evolution in an Immunodeficient Child

Filippi

Amorim

Silva

et al. 2022

Pediatric Infectious Disease Journal

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Background: With the progression of the Coronavirus disease pandemic, the number of mutations in the viral genome has increased, showing the adaptive evolution of severe acute respiratory syndrome coronavirus 2 in humans and intensification in transmissibility. Long-term infections also allow the development of viral diversity. In this study, we report the case of a child with severe combined immu presenting a prolonged severe acute respiratory syndrome coronavirus 2 infection. We aimed to analyze 3 naso-oropharyngeal swab samples collected between August and December 2021 to describe the amino acid changes present in the sequence reads that may have a role in the emergence of new viral variants. Methods: The whole genome from clinical samples was sequenced through high throughput sequencing and analyzed using a workflow to map reads and then find variations/single-nucleotide polymorphisms. In addition, the samples were isolated in cell culture, and a plaque forming units assay was performed, which indicates the presence of viable viral particles. Results: The results obtained showed that the virus present in all samples is infectious. Also, there were 20 common mutations among the 3 sequence reads, found in the ORF1ab and ORF10 proteins. As well, a considerable number of uncommon mutations were found. Conclusions: In conclusion, we emphasize that genomic surveillance can be a useful tool to assess possible evolution signals in long-term patients.

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Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation

Cited by 11 publications

References 18 publications

Early introduction, dispersal and evolution of Delta SARS-CoV-2 in Southern Brazil, late predominance of AY.99.2 and AY.101 related lineages

Early introduction, dispersal and evolution of Delta SARS-CoV-2 in Southern Brazil, late predominance of AY.99.2 and AY.101 related lineages

COVID‐19 in Latin America and the Caribbean: Two years of the pandemic

Prolonged SARS-CoV-2 Infection and Intra-Patient Viral Evolution in an Immunodeficient Child

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