Genomic Surveillance Tracks the First Community Outbreak of the SARS-CoV-2 Delta (B.1.617.2) Variant in Brazil

Lamarca, Alessandra P; Almeida, Luiz Gonzaga Paula de; Francisco, Ronaldo da Silva; Cavalcante, Liliane Tavares de Faria; Machado, Douglas Terra; Brustolini, Otávio J. B.; Gerber, Alexandra Lehmkuhl; Guimarães, Ana P.; Policarpo, Cíntia; Silva, Gleidson da de Oliveira; Boullosa, Lídia Theodoro; Souza, Isabelle Vasconcellos de; Carvalho, Erika Martins de; Ribeiro, Mário Sérgio; Carvalho, Silvia; Silva, Flávio Dias da; Garcia, Márcio Henrique de Oliveira; Souza, Leandro Magalhães de; Silva, Cristiane Gomes da; Ribeiro, Caio Luiz Pereira; Cavalcanti, Andréa Cony; Mello, Claudia Maria Braga de; Tanuri, Amílcar; Vasconcelos, Ana Tereza Ribeiro de

doi:10.1128/jvi.01228-21

Cited by 27 publications

(29 citation statements)

References 6 publications

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“…One month later, this variant was also detected in other capitals, such as Belo Horizonte, Brasília, and São Paulo. A study using random sequencing of samples from patients with COVID-19 described that community transmission of the Delta in Rio de Janeiro possibly started in June, corroborating the results found in our study [ 36 ]. Our results demonstrated that the Delta VOC had become the predominant variant in several capitals such as Rio de Janeiro, São Paulo, Belo Horizonte, Belém, Porto Alegre (considering the 90% predominance cut-off) in September 2021.…”

Section: Discussionsupporting

confidence: 91%

Delta Variant of SARS-CoV-2 Replacement in Brazil: A National Epidemiologic Surveillance Program

Silva

Lima

Alvim

et al. 2022

Viruses

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Coronavirus disease 2019 (COVID-19) pandemic has caused immeasurable impacts on the health and socioeconomic system. The real-time identification and characterization of new Variants of Concern (VOCs) are critical to comprehend its emergence and spread worldwide. In this sense, we carried out a national epidemiological surveillance program in Brazil from April to October 2021. Genotyping by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and sequencing were performed to monitor the dynamics and dissemination of VOCs in samples from 15 federative units. Delta VOC was first detected on June 2021 and took sixteen weeks to replace Gamma. To assess the transmissibility potential of Gamma and Delta VOCs, we studied the dynamics of RT-qPCR cycle threshold (Ct) score in the dominance period of each variant. The data suggest that Delta VOC has a higher transmission rate than Gamma VOC. We also compared relevant symptom patterns in individuals infected with both VOCs. The Delta-infected subjects were less likely to have low oxygen saturation or fatigue, altered results on chest computed tomography, and a propensity for altered X-rays. Altogether, we described the replacement of Gamma by Delta, Delta enhanced transmissibility, and differences in symptom presentation.

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Section: Discussionsupporting

confidence: 91%

Delta Variant of SARS-CoV-2 Replacement in Brazil: A National Epidemiologic Surveillance Program

Silva

Lima

Alvim

et al. 2022

Viruses

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“…The need of oxygen and a lethality rate were observed only in the patients infected by the variants. However, these numbers were below the national (Lamarca et al, 2021) and international average for COVID-19 (Graham et al, 2021), which may be connected to the access and quality of the healthcare provided to the patients from this study, who were monitored daily by phone.…”

Section: Discussionmentioning

confidence: 67%

“…The identification of virus variants was made by viral genome sequencing by the Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, the National laboratory of reference and certified for diagnosis of COVID-19. The methods and techniques for laboratorial diagnostic and sequencing are from national network of surveillance of COVID-19 and were previously published (Faria et al, 2021;Lamarca et al, 2021;Naveca et al, 2021).…”

Section: Study Design and Clinical Samplingmentioning

confidence: 99%

Clinical and epidemiological aspects of patients infected with SARS-CoV-2 variants: a case-control study

Albuquerque

Santos

Torres

et al. 2022

RSD

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Objective: To compare the clinical outcomes of patients infected with SARS-CoV-2 variants with patients infected with the original strain. Methods: This is a case control study comparing cases of COVID-19 patients infected with SARS-CoV-2 variants of concern identified by genomic sequencing, with a control group of 62 patients randomly selected from a COVID-19 database of patients diagnosed prior to the emergence of these variants. Findings: In the 40 patients infected with variants, the predominant (52.5%) was P.1 variant. The variant group presented more arthralgia (p=0.015), hyporexia (p=0.006), nausea/vomiting (p=0.048), and mental confusion (p=0.029), the last not identified in the control group. There were no significant differences in comorbidities or demographic data between the groups. Severe disease, according to the WHO Clinical Progression Scale, was identified only in those infected with the variants, as well as high-flow oxygen therapy and ICU admission (p=0.05). The two deaths reported in the study were in patients infected with the variants. Conclusions: The worst outcomes were observed in the group infected with SARS-CoV-2 variants, although no significant differences in comorbidities or demographics date were observed between the groups.

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“…Our study pointed out that the respiratory symptoms surveillance system is a useful tool that can prevent the transmission of COVID-19 in a public school in a middle-income country such as Brazil. However, during the study period, the Delta variant, which is highly infective, was predominant in the state of São Paulo [9]; no cases of COVID-19 transmission occurred at school. All employees had been fully vaccinated with two doses of the COVID-19 vaccine, and students were vaccinated with at least one dose of the vaccine, which may have had an impact on the low positivity of the participants.…”

Section: Discussionmentioning

confidence: 90%

Online symptoms screening and testing of Covid-19 through RT-LAMP saliva of students and asymptomatic employees in a public school in Brazil.

Costa

Manuli

Oliveira

et al. 2022

Preprint

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Objective To evaluate a respiratory symptoms screening system and test asymptomatic individuals (high school students and employees) at a public school in Brazil. Methods SARS-CoV-2 reverse transcription loop-mediated isothermal amplification (RT-LAMP) of saliva samples was performed weekly. Results A total of 969 samples were tested (mean of 108 tests per week). No asymptomatic participants tested positive for COVID-19, and no cases of COVID-19 transmission occurred at school despite the high transmissibility of the Delta variant, the local predominant variant at the time of the study. Conclusion Implementation of an online system of respiratory symptom screening and testing of COVID-19 through saliva in asymptomatic individuals is a feasible, low-cost and practical option to be used, especially in low-income countries.

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Genomic Surveillance Tracks the First Community Outbreak of the SARS-CoV-2 Delta (B.1.617.2) Variant in Brazil

Cited by 27 publications

References 6 publications

Delta Variant of SARS-CoV-2 Replacement in Brazil: A National Epidemiologic Surveillance Program

Delta Variant of SARS-CoV-2 Replacement in Brazil: A National Epidemiologic Surveillance Program

Clinical and epidemiological aspects of patients infected with SARS-CoV-2 variants: a case-control study

Online symptoms screening and testing of Covid-19 through RT-LAMP saliva of students and asymptomatic employees in a public school in Brazil.

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