Optimization of Illumina AmpliSeq protocol for SARS-CoV-2 and detection of circulating variants in Goiás state, Brazil from november 2020 to july 2021

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dc.creatorBrito, Cíntia Pelegrineti Targueta de Azevedo
dc.creatorFerreira, Ramilla dos Santos Braga
dc.creatorXimenes, Amanda Alves de Melo
dc.creatorCurcio, Juliana Santana de
dc.creatorNunes, Rhewter
dc.creatorDias, Renata de Oliveira
dc.creatorAndrade, Francyelli Mariana dos Santos Mello
dc.creatorSilva, Daniela de Melo e
dc.creatorLacerda, Elisângela de Paula Silveira
dc.creatorCastro, Thaís Guimarães de
dc.creatorPedroso, Thays Millena Alves
dc.creatorPereira, Luiz Augusto
dc.creatorMendonça, Ana Flávia
dc.creatorAlmeida, Robmary Matias de
dc.creatorSilva, Vinicius Lemes da
dc.creatorTelles, Mariana Pires de Campos
dc.date.accessioned2023-02-01T14:17:40Z
dc.date.available2023-02-01T14:17:40Z
dc.date.issued2022
dc.description.abstractThe SARS-CoV-2 pandemic has demonstrated the need for genomic epidemiology surveillance. To date, various methodologies have been applied, including metagenomic approaches and amplicon-based sequencing associated with high-throughput sequencing platforms. We adapted some details in amplicon-based sequencing using a SARS-CoV-2 community panel (Illumina AmpliSeq), with additional modifications for balanced and high-quality sequencing using the MiSeq platform. The modified protocol was used to detect circulating SARS-CoV-2 variants in Goiás state, Brazil. Initially, RNA samples were obtained from swab samples from 15 patients from the state of Goiás, Brazil, in November/2020 and February/2021 to validate protocol steps. The libraries were prepared following AmpliSeq for Illumina workflow with modifications; subsequently, we analyzed 305 positive samples collected from the state of Goiás from December 2020 to July 2021. For protocol improvement, we removed the need to treat samples with DNAse and demonstrated the importance of quantification by qPCR before and after library dilution. No fragmentation pattern was observed in the samples analyzed with Bioanalyzer. The libraries returned sequencing results that were used for genome assembly and variant detection. We were able to assemble SARS-CoV-2 genomes from 318 samples, which were used to identify 13 variants of coronavirus circulating in Goiás throughout those months. Variants of concern, such as Alpha (B.1.1.7), Gamma (P.1) and Delta (B.1.617.2) were detected; the latter was detected at first in Goiás in April 2021. The modifications in the workflow we developed were successfully applied to detect SARS-CoV-2 variants, resulting in high coverage genome assembly, and they can be used to increase the number of genome sequences and aid in epidemiological surveillance in Brazil.pt_BR
dc.identifier.citationTARGUETA, C. P. et al. Optimization of Illumina AmpliSeq protocol for SARS-CoV-2 and detection of circulating variants in Goiás State, Brazil from november 2020 to july 2021. Genetics and Molecular Research, Ribeirão Preto, v. 21, n. 1, p. 1-15, 2022. DOI: 10.4238/gmr19018, Disponível em: https://www.geneticsmr.com/articles/optimization-illumina-ampliseq-protocol-sars-cov-2-and-detection-circulating-variants-goi-s. Acesso em: 25 jan. 2023.pt_BR
dc.identifier.doi10.4238/gmr19018
dc.identifier.issne- 1676-5680
dc.identifier.urihttp://repositorio.bc.ufg.br/handle/ri/21827
dc.language.isoengpt_BR
dc.publisher.countryBrasilpt_BR
dc.publisher.departmentInstituto de Ciências Biológicas - ICB (RG)pt_BR
dc.rightsAcesso Abertopt_BR
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.subjectAmpliSeqpt_BR
dc.subjectAmplicon sequencingpt_BR
dc.subjectCoronaviruspt_BR
dc.subjectViral genomept_BR
dc.subjectCOVID-19pt_BR
dc.subjectHigh-throughput sequencingpt_BR
dc.titleOptimization of Illumina AmpliSeq protocol for SARS-CoV-2 and detection of circulating variants in Goiás state, Brazil from november 2020 to july 2021pt_BR
dc.typeArtigopt_BR

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