SARS-CoV-2 Delta variant of concern in Brazil - multiple introductions, communitary transmission, and early signs of local evolution

Patané, José Salvatore Leister; Viala, Vincent Louis; Lima, Loyze Paola Oliveira de; Martins, Antonio Jorge; Barros, Cláudia; Marqueze, Elaine Cristina; Bernardino, Jardelina de Souza Todão; Moretti, Débora Botéquio; Slavov, Svetoslav Nanev; Bezerra, Rafael dos Santos; Rodrigues, Evandra Strazza; Santos, Elaine Vieira; Brassaloti, Ricardo Augusto; Cassano, Raquel de Lello Rocha Campos; Mariani, Pilar Drummond Sampaio Corrêa; Kitajima, João Paulo; Santos, Bibiana; Assato, Patrícia Akemi; Costa, Felipe da Silva da Allan; Poleti, Mirele Daiana; Lesbon, Jéssika Cristina Chagas; Chicaroni, Elisangela; Banho, Cecília Ártico; Sacchetto, Lívia; Moraes, Marília Mazzi; Palmieri, Massimiliano; Vilanova, Fabiana; Martininghi, Maiara; Grotto, Rejane Tommasini; Souza-Neto, Jayme A.; Giovanetti, Marta; Alcântara, Luiz Carlos Júnior; Nogueira, Maurício Lacerda; Fukumasu, Heidge; Coutinho, Luiz Lehmann; Calado, Rodrigo T.; Kashima, Simone; Machado, Roseli de Oliveira; Covas, Dimas Tadeu; Elias, Carolina; Coccuzzo, Sandra

doi:10.1101/2021.09.15.21262846

Cited by 15 publications

(18 citation statements)

References 6 publications

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“…Considering this limitation, it was not possible to assess the introduction of Delta or possible cases of Omicron in the study population. The introduction and replacement of Gamma in the Brazilian population by Delta occurred in the second half of 2021 13 …”

Section: Discussionmentioning

confidence: 99%

Use of saliva and RT‐PCR screening for SARS‐CoV‐2 variants of concern: Surveillance and monitoring

Zerbinati

Palmieri

Schwab

et al. 2022

Journal of Medical Virology

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Genomic surveillance has been applied since the beginning of the COVID-19 pandemic to track the spread of the virus, leading to the characterization of multiple SARS-CoV-2 variants, including variants of concern (VOC). Although sequencing is the standard method, a rapid molecular test for screening and surveillance of VOC is considered for detection. Furthermore, using alternative saliva as specimen collection facilitates the implementation of a less invasive, self-collected sample.In this study, we applied a combinatory strategy of saliva collection and reverse transcription polymerase chain reaction (RT-PCR) for SARS-CoV-2 VOC detection.Saliva samples from patients attending a tertiary hospital with suspected COVID-19 were collected and SARS-CoV-2 RNA was detected using SARS-CoV-2 RT-qPCR reagent kit (PerkinElmer). Positive saliva samples were screened for SARS-CoV-2 VOC with previously described RT-PCR for Alpha, Beta, and Gamma variants. Saliva samples were positive in 171 (53%) of 324 tested. A total of 108 (74%) from positive samples were also positive for VOC by RT-PCR screening. Those samples were found between January and August 2021. This approach allowed us to successfully use an alternative and complementary tool to genomic surveillance to monitor the circulation of SARS-CoV-2 VOC in the studied population.

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Section: Discussionmentioning

confidence: 99%

Use of saliva and RT‐PCR screening for SARS‐CoV‐2 variants of concern: Surveillance and monitoring

Zerbinati

Palmieri

Schwab

et al. 2022

Journal of Medical Virology

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“…In Brazil, on the background of this solid process of vaccination, the first cases of Delta variant of concern (VOC) introductions were reported. 1 Despite the full substitution of the pre‐existing Gamma VOC in Brazil with the Delta VOC, no exponential growth of the new cases has been observed, most probably due to the ongoing vaccination. Delta VOC is highly diversified, and more than 120 sublineages have been classified within the Pango lineages ( https://cov-lineages.org/ ) with the continuous description of novel lineages and sublineages.…”

Section: Introductionmentioning

confidence: 99%

“…Currently in Brazil have been applied more than 381 million doses of anti‐severe acute respiratory syndrome coronavirus‐2 (anti‐SARS‐CoV‐2) vaccines and the individuals who have been fully vaccinated are bordering 140 million, which makes Brazil one of the most vaccinated nations in the world (https://www.gov.br/saude/pt-br/vacinacao). In Brazil, on the background of this solid process of vaccination, the first cases of Delta variant of concern (VOC) introductions were reported 1 . Despite the full substitution of the pre‐existing Gamma VOC in Brazil with the Delta VOC, no exponential growth of the new cases has been observed, most probably due to the ongoing vaccination.…”

Section: Introductionmentioning

confidence: 99%

SARS‐COV‐2 genomic monitoring in the state of São Paulo unveils two emerging AY.43 sublineages

Lima

Ribeiro

Viala

et al. 2022

Journal of Medical Virology

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Delta VOC is highly diverse with more than 120 sublineages already described as of November 30, 2021. In this study, through active monitoring of circulating severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) variants in the state of São Paulo, southeast Brazil, we identified two emerging sublineages from the ancestral AY.43 strain which were classified as AY.43.1 and AY.43.2. These sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for the AY.43.1 and ORF1ab:G1155C for the AY.43.2 and our analysis reveals that they might have a likely‐Brazilian origin. Much is still unknown regarding their dissemination in the state of São Paulo and Brazil as well as their potential impact on the ongoing vaccination process. However, the results obtained in this study reinforce the importance of genomic surveillance activity for timely identification of emerging SARS‐CoV‐2 variants which can impact the ongoing SARS‐CoV‐2 vaccination and public health policies.

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“…To identify the circulating SARS-CoV-2 variants in the state of São Paulo, the Butantan Network for Pandemic Alert of SARS-CoV-2 Variant (Butantan Network) was established in March 2021, provided high throughput sequencing of SARS-CoV-2 of this Brazilian region. Of note, this network was responsible for the detection of the first cases of the Beta VOC (B.1.351) in Brazil [ 4 ], Lambda variant of interest (VOI) (C.37) in the State of São Paulo [ 5 ], and the initial steps of Delta VOC (B.1.617.2) introduction [ 2 , 6 ].…”

Section: Introductionmentioning

confidence: 99%

The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela

Viala

Slavov

Lima

et al. 2022

Viruses

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Our effort in SARS-CoV-2 genomic surveillance in Brazil has detected the Alpha Variant of Concern with a predominance higher than 75% in the population of Ilhabela island (São Paulo State) at a time when the Gamma VOC was already predominating the mainland raised concerns for closer surveillance on this island. Therefore, we intensified the surveillance for 24 weeks by generating data from 34% of local positive cases. Our data show that the patterns of VOC predominance dynamics and infection rates were in general distinct from the mainland. We report here the first known case of Alpha predominance in a Brazilian population, a delay greater than 3 months for the Gamma to dominate the previous variants compared to the mainland, and a faster dispersion rate of Gamma and Delta VOCs compared to the mainland. Phylogenetic analysis revealed the SARS-CoV-2 transmission dynamics in Ilhabela were characterized by multiple independent introduction events of Gamma and Delta, with a few events of Alpha introduction, two of them followed by community transmission. This study evidenced the peculiar behavior of SARS-CoV-2 variants in an isolated population and brought to light the importance of specific programs for SARS-CoV-2 genomic surveillance in isolated populations.

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SARS-CoV-2 Delta variant of concern in Brazil - multiple introductions, communitary transmission, and early signs of local evolution

Cited by 15 publications

References 6 publications

Use of saliva and RT‐PCR screening for SARS‐CoV‐2 variants of concern: Surveillance and monitoring

Use of saliva and RT‐PCR screening for SARS‐CoV‐2 variants of concern: Surveillance and monitoring

SARS‐COV‐2 genomic monitoring in the state of São Paulo unveils two emerging AY.43 sublineages

The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela

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