Banca de DEFESA: LUIZ RICARDO FRASER SILVA

Uma banca de DEFESA de MESTRADO foi cadastrada pelo programa.
STUDENT : LUIZ RICARDO FRASER SILVA
DATE: 05/10/2023
TIME: 14:00
LOCAL: Instituto de Ciências da Saúde, UFBA
TITLE:

A comparative evaluation of automated platforms for assembly and analysis of SARS-CoV-2 genomes

KEY WORDS:

SARS-CoV-2, Genomic surveillance, Ampliseq, RNA-seq

PAGES: 85
BIG AREA: Ciências Biológicas
AREA: Microbiologia
SUMMARY:

The COVID-19 pandemic, caused by the SARS-CoV-2 virus (Severe Acute Respiratory Syndrome Coronavirus 2), began in the province of Wuhan in China and quickly spread around the globe, generating socioeconomic and public health impacts. The discovery of the viral agent causing the disease was only possible thanks to new nucleic acid sequencing technologies, collectively known as NGS (Next Generation Sequencing). Currently, these same technologies are being used for genomic surveillance of the virus, including the identification of mutations and determination of new variants. In 2022, the World Health Organization issued a global genomic surveillance strategy for potentially pandemic and epidemic pathogens (2022-2032). In order to contribute to this strategy and improve access to viral detection tools, the main objective of this work is to implement, compare, and validate analysis protocols using only raw NGS data (FASTQ files) for the diagnosis and variant calling of SARS-CoV-2. For this purpose, a total of 15 new SARS-CoV-2 sequencing samples obtained by Ion AmpliSeq targeted methodology (n=10) or metatranscriptomic approach (n=5) were used as the sample universe. These FASTQ files were subjected to assembly using the automated assemblers: PATRIC, BV-BRC, ID-seq, CoronaSPAdes, and Genome Detective. Variant calling was performed using the platforms GISAID, Genome Detective, Nextclade, and BV-BRC, which have an integrated approach to assembly and annotation. The analyses were carried out at two different time points to identify possible changes in the results after platform updates. The generated results were compared, among other aspects, in terms of the ability to call SARS-CoV-2 variants, the average time spent on analysis, identified viral ORFs (Open Reading Frames), and the percentage of G+C content in the assembled genome. Initially, the BV-BRC platform proved to be capable of correctly determining the variant, with the highest number of results generated in the shortest time. ID-seq and Genome Detective were able to perform genome assembly, and from the generated FASTA files, variant calling was performed using the Nextclade platform and Genome Detective itself for annotation. After updates, BV-BRC, despite still producing the highest number of results in the shortest time, showed lower specificity in variant calling. However, Genome Detective presented an integrated approach to assembly and annotation with a greater ability to determine the variant. The assembler PATRIC and the annotation platform GISAID were not able to generate satisfactory results for the evaluated samples.

COMMITTEE MEMBERS:
Presidente - 1818609 - LUIS GUSTAVO CARVALHO PACHECO
Interno - ***.842.665-** - GUBIO SOARES CAMPOS - UFBA
Externa à Instituição - BRENA MOTA MOITINHO SANT'ANNA - UFBA