Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon

Sgorlon, Gabriella; Queiroz, Jackson Alves da Silva; Roca, Tárcio Peixoto; Silva, Ana Maisa Passos da; Gasparelo, Nadson Willian Felipe; Teixeira, Karolaine Santos; Oliveira, Andreia Souza da Nóbrega; Mendonça, Aline Linhares Ferreira de Melo; Maia, Adriana Cristina Salvador; Pereira, Soraya dos Santos; Batista, Flávia Serrano; Salcêdo, Juan Miguel Villalobos; Rampazzo, Rita de Cássia Pontello; Resende, Paola Cristina; Siqueira, Marilda Mendonça; Naveca, Felipe Gomes; Vieira, Deusilene Souza

doi:10.1590/0074-02760220155

Cited by 5 publications

(6 citation statements)

References 45 publications

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“…Minas Gerais, a state bordering Rio de Janeiro, reported 73% of Delta variant infections in September, specifically during EW 37 [39]. In October, the Tocantins [57] and Rondônia [58] states in the northern region of Brazil also reached the same percentage mark. Interestingly, the state of Pará, situated along the border with Tocantins, registered infection with the Gamma variant up until July 2022 [59].…”

Section: Discussionmentioning

confidence: 95%

Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis

y Castro,

Piccoli,

Vieira

et al. 2023

Microorganisms

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Mutations in the SARS-CoV-2 genome can alter the virus’ fitness, leading to the emergence of variants of concern (VOC). In Brazil, the Gamma variant dominated the pandemic in the first half of 2021, and from June onwards, the first cases of Delta infection were documented. Here, we investigate the introduction and dispersal of the Delta variant in the RS state by sequencing 1077 SARS-CoV-2-positive samples from June to October 2021. Of these samples, 34.7% were identified as Gamma and 65.3% as Delta. Notably, 99.2% of Delta sequences were clustered within the 21J lineage, forming a significant Brazilian clade. The estimated clock rate was 5.97 × 10−4 substitutions per site per year. The Delta variant was first reported on 17 June in the Vinhedos Basalto microregion and rapidly spread, accounting for over 70% of cases within nine weeks. Despite this, the number of cases and deaths remained stable, possibly due to vaccination, prior infections, and the continued mandatory mask use. In conclusion, our study provides insights into the Delta variant circulating in the RS state, highlighting the importance of genomic surveillance for monitoring viral evolution, even when the impact of new variants may be less severe in a given region.

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Section: Discussionmentioning

confidence: 95%

Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis

y Castro,

Piccoli,

Vieira

et al. 2023

Microorganisms

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“…21,22 The Gamma variant was quickly replaced in Rondônia by the Delta variant; however, it was not responsible for new waves of cases like those previously reported. 23,24 A smaller number of individuals appear related to the Omicron variant reported lately as an alert. 25 In Rondônia, the rate of sequenced samples was satisfactory in all health regions compared with other regions of the country, keeping genomic surveillance levels active.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia

Sgorlon

Roca

Passos-Silva

et al. 2023

Bioinform Biol Insights

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The increased transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has generated variants of concern (VOCs) throughout the pandemic, responsible for waves of cases worldwide. To monitor mutations in the S gene of SARS-CoV-2 in different variants, we evaluated 1497 individuals with COVID-19 in western Amazonia in the period April 2021 to July 2022. The epidemiological and clinical data of the individuals were collected; subsequently, the samples were extracted using a commercial kit, the viral load was assessed, and viral genomes were sequenced. We analyzed the quality and mutations of the genomes and maximum likelihood phylogenetic inference. However, 3 main clusters were observed, referring to Gamma (52.91%), Delta (24.38%), and Omicron (20.38%) VOCs with wide distribution in all health regions of the Rondônia state. Regarding the vaccination profile, there was a higher percentage of unvaccinated and partially vaccinated individuals, with more representatives by the Gamma variant. A total of 1412 sequences were suitable for mutation analysis in the S gene region. The Omicron VOC showed 38 mutations, with the Delta and Gamma variants with 16 and 17, respectively. The VOC Omicron and Gamma shared 4 mutations E484K, H655Y, N501Y, and N679K with high frequency, and Delta and Omicron 2 mutations (T478K and T95I). Regarding the comparison between the frequency of mutations for each variant concerning the vaccination groups, there were no changes in mutations for each group. In conclusion, the study showed a temporal increase in mutations and subvariants for characterized strains. Furthermore, the vaccination profile did not impact significant changes in the mutational profile yet remains a determining factor for severe disease.

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“…These patients were under Delta or Gamma infection in Brazil. 16 , 17 According to the Brazilian Epidemiological Monitoring Guidelines for the Public Health Emergency of COVID-19 published by the Brazilian Ministry of Health on April 3, 2020, 16 , they were out of the isolation period. Patients were recruited for this study from two sources: those hospitalised in the local referral centre for the treatment of COVID-19 patients after hospital discharge (Mário Covas State Hospital, Santo André, São Paulo Metropolitan Area, Brazil) and health-care workers from the Centro Universitário (FMABC, Santo André, São Paulo Metropolitan Area, Brazil).…”

Section: Methodsmentioning

confidence: 99%

Ophthalmic Manifestations Among Patients Surviving COVID-19

Lima¹,

Soares²,

Pereira³

et al. 2023

IJGM

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Background and Aim To identify ocular findings related to SARS-CoV-2 infection in patients after the resolution of COVID-19 using complete ocular examinations and optical coherence tomography (OCT). Methods In this cross-sectional study, conducted from May 30 to October 30, 2020, patients who recovered from various stages COVID-19 underwent eye examination and multimodal retinal imaging (Retinographies and Spectral-OCT). Results We included 50 patients, 29 (58%) males, median age of 46.5 [standard deviation 15.8]. Of these, 42% (21) had mild, 18% (9) had severe and 40% (20) had critical disease. The median time interquartile range (IQR) between symptom onset and ocular examination was 55 days [IQR 39–71]. Seven patients (14%) reported ophthalmic symptoms, transitory low visual acuity (6%) and retroocular pain (8%). On OCT, one patient without comorbidities had sectoral retinal pallor suggestive of acute retinal ischaemia and oedema of the retina’s inner layers and atrophy. All findings progressively and spontaneously improved months after resolution of COVID-19. Conclusion Patients with COVID-19 present findings compatible with the general population depending on age and comorbidities; nevertheless, acute retinal findings associated with the disease may be present, such as caused either by the direct effects of retinal SARS-CoV-2 infection, by indirect effects of the cytokine storm or by the pro-thrombotic state associated with COVID-19. Therefore, retinal involvement in patients with COVID-19 remains subject to considerable discussion and study.

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Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon

Cited by 5 publications

References 45 publications

Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis

Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis

SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia

Ophthalmic Manifestations Among Patients Surviving COVID-19

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