ViralFlow v1.0—a computational workflow for streamlining viral genomic surveillance

da Silva, Alexandre Freitas; da Silva Neto, Antonio Marinho; Aksenen, Cleber Furtado; Jeronimo, Pedro Miguel Carneiro; Dezordi, Filipe Zimmer; Almeida, Suzana Porto; Costa, Hudson Marques Paula; Salvato, Richard Steiner; Campos, Tulio de Lima; Wallau, Gabriel da Luz; of the Fiocruz Genomic Network, on behalf

doi:10.1093/nargab/lqae056

Cited by 8 publications

(2 citation statements)

References 29 publications

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“…The libraries were then sequenced on the Illumina MiSeq platform using Illumina MiSeq V3 600 cycle kits. Raw sequencing data in FASTQ format were processed through the ViralFlow pipeline (https://viralflow.github.io/), providing a comprehensive workflow for referenced-based assembly, quality control, variant calling, and consensus sequence generation (19).…”

Section: Methodsmentioning

confidence: 99%

Endemic transmission and international introduction of Monkeypox virus in Southern Brazil between 2022-2023

Godinho,

Bermann,

de Oliveira

et al. 2024

Preprint

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Mpox is a zoonotic viral disease caused by the monkeypox virus (MPXV). Human cases have been mainly restricted to the African continent until the worldwide multi-country outbreak unfolded in 2022. We reconstructed epidemiological links of MPXV infections using genomic epidemiology in Rio Grande do Sul State, southern Brazil, during 2022 and 2023. We detected five well-supported clades, three representing local transmission chains that were mostly restricted to the 2022 virus spread, one supported year-long maintenance encompassing samples from 2022 and 2023, and one new importation from Europe in 2023. Our results provide new insights into the geographic extent of community transmission and its association with viral diversity during the more pronounced 2022 mpox upsurge and during the following lower incidence endemic transmission phase. These findings highlight the power of continued genomic surveillance to uncover hidden transmission chains to understand viral dynamics and inform public health responses. The detection of sustained endemic transmission in the state is important to guide targeted control measures to curtail further community and international transmission and highlight the need for strengthening genomic surveillance.

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Section: Methodsmentioning

confidence: 99%

Endemic transmission and international introduction of Monkeypox virus in Southern Brazil between 2022-2023

Godinho,

Bermann,

de Oliveira

et al. 2024

Preprint

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“…The genomes were assembled using a reference-guided strategy with the ViralFlow v.1.2.0 pipeline 13 for each of the three OROV segments (L -OL689334.1, M -OL689333.1 and S segments -OL689332.1). Sequences were deposited in GenBank (accession numbers: PQ073181-PQ073186).…”

Section: Genome Assembly and Phylogenetic Analysismentioning

confidence: 99%

Genomic and phenotypic characterization of an Oropouche virus strain implicated in the 2023-24 large-scale outbreak in Brazil

Azevedo,

da Silva,

da Silva

et al. 2024

Preprint

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TheOrthobunyavirus oropoucheensein a arthropod borne zoonotic pathogen known to infect sylvatic animals and humans by means of biting midges transmission. Several large-scale human outbreaks of Oropouche virus (OROV), primarily confined to the Amazon region, were documented over the decades. However, since 2022, more widespread OROV outbreaks have been unfolding in Brazil and across South America, with cases exported to Cuba, Italy, and Germany. I In Brazil, the virus has reached and established communitary transmission in states from all major regions of the country. Here we isolated, characterized the cytopathic effect and the full genomic sequence of two OROV isolates from the current outbreak. Our data shows that OROV can readily infect and replicate in non-human primate cells, supporting the role of non-human primates as important reservoirs. Phylogenetic data supports a direct introduction of the same lineages causing the 2022-24 outbreak in Brazil from the Amazonas state, the epicenter of the epidemics in Brazil. Lastly, as case counts accumulate in the state and the Northeast region, clear evidence supports established and sustained transmission. Continued studies are critical to understand the transmission cycle in this region, the most important vectors and reservoirs, to appropriately deploy control measures.

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Genomic and phenotypic characterization of the Oropouche virus strain implicated in the 2022–24 large‐scale outbreak in Brazil

Azevedo,

Silva,

Silva

et al. 2024

Journal of Medical Virology

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The Orthobunyavirus oropoucheense species encompasses a group of arthropod‐borne zoonotic viruses transmitted by biting midges to animals including humans. Several large‐scale human outbreaks caused by the prototype member of this species, Oropouche virus (OROV) have been documented since the 1970s and were primarily confined to the Amazon basin. However, since 2022, more widespread OROV outbreaks have been unfolding in Brazil and across South America, with cases exported to Cuba, Italy, Spain, USA and Germany. In Brazil, the virus has reached and established communitary transmission in all geographic areas of the country. We isolated, characterized the cytopathic effect and recovered the full genome of two OROV isolates from the 2022–24 outbreak detected in patients from the Pernambuco state. Phylogenetic data supports a direct introduction from the Amazonas state, the epicenter of the epidemics in the country. As case counts accumulate in the state mounting evidence is supporting the establishiment of sustained transmission chains. Continued studies are critical to understand the transmission cycle in this region, including the most important vectors and reservoirs, to appropriately deploy control measures.

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ViralFlow v1.0—a computational workflow for streamlining viral genomic surveillance

Cited by 8 publications

References 29 publications

Endemic transmission and international introduction of Monkeypox virus in Southern Brazil between 2022-2023

Endemic transmission and international introduction of Monkeypox virus in Southern Brazil between 2022-2023

Genomic and phenotypic characterization of an Oropouche virus strain implicated in the 2023-24 large-scale outbreak in Brazil

Genomic and phenotypic characterization of the Oropouche virus strain implicated in the 2022–24 large‐scale outbreak in Brazil

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