Dataset Information

Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022.

ABSTRACT: Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation.

SUBMITTER: Claro IM

PROVIDER: S-EPMC9217064 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022.

Claro Ingra Morales IM Romano Camila Malta CM Candido Darlan da Silva DDS Lima Evelyn Lepka de EL Lindoso José Angelo Lauletta JAL Ramundo Mariana Severo MS Moreira Filipe Romero Rebello FRR Barra Luiz Alberto Costa LAC Borges Luciana Marques Sansão LMS Medeiros Lucas Alberto LA Tomishige Marcia Y S MYS Moutinho Tomas T Silva Anderson José Dias da AJDD Rodrigues Camila Cristina Martini CCM Azevedo Luiz Cesar Fernandes de LCF Villas-Boas Lucy Santos LS Silva Camila Alves Maia da CAMD Coletti Thaís Moura TM Manuli Erika R ER O'Toole Aine A Quick Joshua J Loman Nicholas N Rambaut Andrew A Faria Nuno R NR Figueiredo-Mello Claudia C Sabino Ester Cerdeira EC

Revista do Instituto de Medicina Tropical de Sao Paulo 20220624

Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation. ...[more]

PMID: 35749419

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Project description:Dengue virus (DENV) represents a public health threat and economic burden in affected countries. The availability of genomic data is key to understanding viral evolution and dynamics, supporting improved control strategies. Currently, the use of high-throughput sequencing (HTS) technologies, which can be applied both directly to patient samples (shotgun metagenomics) and to PCR-amplified viral sequences (amplicon sequencing), is potentially the most informative approach to monitor viral dissemination and genetic diversity by providing, in a single methodological step, identification and characterization of the whole viral genome at the nucleotide level. Despite many advantages, these technologies require bioinformatics expertise and appropriate infrastructure for the analysis and interpretation of the resulting data. In addition, the many software solutions available can hamper the reproducibility and comparison of results. Here we present DEN-IM, a one-stop, user-friendly, containerized and reproducible workflow for the analysis of DENV short-read sequencing data from both amplicon and shotgun metagenomics approaches. It is able to infer the DENV coding sequence (CDS), identify the serotype and genotype, and generate a phylogenetic tree. It can easily be run on any UNIX-like system, from local machines to high-performance computing clusters, performing a comprehensive analysis without the requirement for extensive bioinformatics expertise. Using DEN-IM, we successfully analysed two types of DENV datasets. The first comprised 25 shotgun metagenomic sequencing samples from patients with variable serotypes and genotypes, including an in vitro spiked sample containing the four known serotypes. The second consisted of 106 paired-end and 76 single-end amplicon sequences of DENV 3 genotype III and DENV 1 genotype I, respectively, where DEN-IM allowed detection of the intra-genotype diversity. The DEN-IM workflow, parameters and execution configuration files, and documentation are freely available at https://github.com/B-UMMI/DEN-IM).

Dataset Information

Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022.

Publications

Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022.

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