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SARS-COV-2 SEQUENCING AND VARIANTS IDENTIFICATION FOR GENOMIC SURVEILLANCE AND MOLECULAR EPIDEMIOLOGY

Published in 26/04/2022 - ISBN: 978-65-5941-645-5

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Paper Title
SARS-COV-2 SEQUENCING AND VARIANTS IDENTIFICATION FOR GENOMIC SURVEILLANCE AND MOLECULAR EPIDEMIOLOGY
Authors
  • Erick Gustavo Dorlass
  • Deyvid Amgarten
  • Tania Girão Mangolini
  • Fernanda de Mello Malta
  • Nair Hideko Muto
  • Anelisie da Silva Santos
  • Marcio Anunciacao Menezes
  • Alexandre Hideaki Takara
  • Ana Paula Moreira Salles
  • Roberta Cardoso Petroni
  • João Renato Rebello Pinho
  • Murilo Cervato
Modality
Xpress presentation
Subject area
Omics
Publishing Date
26/04/2022
Country of Publishing
Brasil
Language of Publishing
Inglês
Paper Page
https://www.even3.com.br/anais/xmeetingxp2021/414636-sars-cov-2-sequencing-and-variants-identification-for-genomic-surveillance-and-molecular-epidemiology
ISBN
978-65-5941-645-5
Keywords
Virus, Next-Generation Sequencing, SARS-CoV-2
Summary
Since December 2019, SARS-CoV-2 has claimed over 4 million lives worldwide with more than 500,000 deaths in Brazil. As the virus spreads and evolves, a great number of variants emerge and become dominant over the pre-existing ones. The genomic diversification of the virus can result in higher infection rate and weaker immune response by vaccinated individuals against new variants. Therefore, genomic surveillance can be used for new variants identification and tracking. Here we performed identification of SARS-CoV-2 variants in clinical samples sequenced by Illumina thecnology using a Cromwell orchestrated pipeline in Amazon AWS cloud service. Raw FASTQ files are submitted to an Amazon AWS bucket with a Lambda function triggered by each individual upload. When triggered, a Cromwell orchestrated pipeline is activated, scaling spot EC2 instances for maintaining performance through all pipeline execution regardless of the number of submitted FASTQ files. Briefly, the pipeline performs: 1. Filtering and trimming of sequences for quality control. 2. Mapping the resulting sequences to SARS-CoV-2 reference genome. 3. Variant calling using GATK Haplotype with custom parameters. 4. Whole genome consensus generation and 5. Lineage identification with Pangolin software. To date, we analyzed 1,296 sequences obtained since march 2020 from clinical samples in Hospital Israelita Albert Einstein. We managed to obtain 1,165 of complete sequences, most of them uploaded to GISAID’s EpiCoV database. Average coverage for all samples is 5,882x with 99.91% of the genome coverage at least 10x. From March to october 2020, the main variants detected were B.1.1.28 and B.1.1.33. In November the P.2 (Zeta) variant emerged and became dominant until January 2021, when the Variant of Concern (VOC) P.1 (Gamma), emerged and became dominant even with the introduction and circulation of the VOC B.1.1.7 (Alpha). The Gama variant became dominant until August 2021, when the Delta variant emerged. Other variants derived from the Gama lineage were detected in the meantime such as P.1.2 and P.1.7. The last one had a peak on its circulation detection in August 2021. Besides VOCs, our method also detected Variants of Interest (VOIs) such as C.37 (Lambda) and B.1.621 (Mu) and other variants like B.1.629, B.1.1.44, B.1.1.29, B.1.1.8, B.1.1.274, B.1.1.143 and others. A real time display of our obtained results are available in https://sarsomics.com/dashboard/. The uprising of the Gamma and Delta variant as the detection of the Alpha variant also suggest a flaw in the established public health measurements for containing the virus circulation. In conclusion, our genomic surveillance showed the continuous appearance of Variants of Concern or Interest as they emerged over time harboring important mutations for viral fitness. Also, the genomic surveillance proved to be an important tool for evaluating the public health efforts implemented for SARS-CoV-2 contention.
Title of the Event
X-Meeting XPerience 2021
Title of the Proceedings of the event
X-Meeting presentations
Name of the Publisher
Even3
Means of Dissemination
Meio Digital
DOI
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How to cite

DORLASS, Erick Gustavo et al.. SARS-COV-2 SEQUENCING AND VARIANTS IDENTIFICATION FOR GENOMIC SURVEILLANCE AND MOLECULAR EPIDEMIOLOGY.. In: X-Meeting presentations. Anais...São Paulo(SP) AB3C, 2021. Available in: https//www.even3.com.br/anais/xmeetingxp2021/414636-SARS-COV-2-SEQUENCING-AND-VARIANTS-IDENTIFICATION-FOR-GENOMIC-SURVEILLANCE-AND-MOLECULAR-EPIDEMIOLOGY. Access in: 27/07/2024

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