Mary Wilson
Well-known member
June 9 2022
Ingra Morales Claro, Evelyn Lepka de Lima, Camila Malta Romano, Darlan da Silva Candido, José Angelo Lauletta Lindoso, Luiz Alberto Costa Barra, Luciana Marques Sansão Borges, Lucas Alberto Medeiros, Marcia Y. S. Tomishige, Mariana Severo Ramundo, Tomas Moutinho, Lucy Santos Villas-Boas, Camila A. M. da Silva, Thaís M. Coletti, Aine O’Toole, Nick Loman, Andrew Rambaut, Nuno R. Faria, Claudia Figueiredo-Mello, Ester C. Sabino
... As of the 8th of June, 2022, Brazil had 8 suspected monkeypox infections in the States of Santa Catarina, Ceará, Mato Grosso do Sul, Rio Grande do Sul, Rondônia and São Paulo (Brazilian Ministry of Health 2022).
Here we report a near complete genome of the first confirmed monkeypox case detected in Brazil. A skin swab of the lesions (vesicle and crust) was collected on June 7th, 2022 at Emilio Ribas Institute of Infectious diseases, from a male patient, aged 41 years old, and with a recent travel history to Portugal and Spain.
... Genome sequencing was performed upon sample receipt at the Institute Tropical Medicine, Sao Paulo, on the 7th June, and sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation. Results were shared immediately upon generation and quality control with the patient’s healthcare facility and local public health authorities, and confirmed 24h later in a reference laboratory. Our sequencing run generated a total of 954,284 reads, with 784,000 reads with quality score > 8 used in the following analysis. The percentage of mapped reads was ~2%, with an average depth of 277.7x, covering 100% of the viral genome with at least 1 read, with an N50 of 4,493. The consensus sequence and raw data can also be found in our project’s dedicated GitHub repository (GitHub - CADDE-CENTRE/Monkeypox: Monkeypox data 8). Complete MPXV genome sequence has also been submitted to NCBI GenBank.
To contextualise the novel monkeypox genome, we downloaded 102 whole-genome sequences from NCBI GenBank (Extended data - Table S1). Of these, 81 were genomes from the ongoing multi-country outbreaks. The dataset was aligned to the reference genome using MAFFT version 7·453 (Katoh & Standley 2013) 1. ...
https://virological.org/t/first-monkeypox-virus-genome-sequence-from-brazil/850#post_1
Ingra Morales Claro, Evelyn Lepka de Lima, Camila Malta Romano, Darlan da Silva Candido, José Angelo Lauletta Lindoso, Luiz Alberto Costa Barra, Luciana Marques Sansão Borges, Lucas Alberto Medeiros, Marcia Y. S. Tomishige, Mariana Severo Ramundo, Tomas Moutinho, Lucy Santos Villas-Boas, Camila A. M. da Silva, Thaís M. Coletti, Aine O’Toole, Nick Loman, Andrew Rambaut, Nuno R. Faria, Claudia Figueiredo-Mello, Ester C. Sabino
... As of the 8th of June, 2022, Brazil had 8 suspected monkeypox infections in the States of Santa Catarina, Ceará, Mato Grosso do Sul, Rio Grande do Sul, Rondônia and São Paulo (Brazilian Ministry of Health 2022).
Here we report a near complete genome of the first confirmed monkeypox case detected in Brazil. A skin swab of the lesions (vesicle and crust) was collected on June 7th, 2022 at Emilio Ribas Institute of Infectious diseases, from a male patient, aged 41 years old, and with a recent travel history to Portugal and Spain.
... Genome sequencing was performed upon sample receipt at the Institute Tropical Medicine, Sao Paulo, on the 7th June, and sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation. Results were shared immediately upon generation and quality control with the patient’s healthcare facility and local public health authorities, and confirmed 24h later in a reference laboratory. Our sequencing run generated a total of 954,284 reads, with 784,000 reads with quality score > 8 used in the following analysis. The percentage of mapped reads was ~2%, with an average depth of 277.7x, covering 100% of the viral genome with at least 1 read, with an N50 of 4,493. The consensus sequence and raw data can also be found in our project’s dedicated GitHub repository (GitHub - CADDE-CENTRE/Monkeypox: Monkeypox data 8). Complete MPXV genome sequence has also been submitted to NCBI GenBank.
To contextualise the novel monkeypox genome, we downloaded 102 whole-genome sequences from NCBI GenBank (Extended data - Table S1). Of these, 81 were genomes from the ongoing multi-country outbreaks. The dataset was aligned to the reference genome using MAFFT version 7·453 (Katoh & Standley 2013) 1. ...
https://virological.org/t/first-monkeypox-virus-genome-sequence-from-brazil/850#post_1