Complete Coding Sequences of 23 South African Domestic and Wildlife Rabies Viruses

Sabeta, Claude; Mohale, Debrah; Phahladira, Baby; Ngoepe, Ernest; Schalkwyk, Antoinette van; Mogano, Kgaogelo; Chirima, George; Suzuki, Toru; Makita, Kohei

doi:10.1128/mra.00621-20

Cited by 4 publications

(4 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The remaining samples had 1-14 'non-haploid' sites, and the same such site could be observed in a maximum of two samples. RABV-GLUE identified the samples as the cosmopolitan AF1b lineage (Table 5), agreeing with the originally reported classification [44].…”

Section: Plos Onesupporting

confidence: 90%

“…To demonstrate that our approach can process not only AmpliSeq datasets, we run the Rabies virus (RABV) dataset presented by Sabeta et al (2020) [44] through our pipeline. Sequencing reads of this dataset were obtained after the depletion of host DNA and RNA [44]. To genotype the samples of this dataset, we used the genome of Rabies virus (isolate 20034) (KT336433).…”

Section: Plos Onementioning

confidence: 99%

See 1 more Smart Citation

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data

et al. 2022

View full text Add to dashboard Cite

The most important information about microorganisms might be their accurate genome sequence. Using current Next Generation Sequencing methods, sequencing data can be generated at an unprecedented pace. However, we still lack tools for the automated and accurate reference-based genotyping of viral sequencing reads. This paper presents our pipeline designed to reconstruct the dominant consensus genome of viral samples and analyze their within-host variability. We benchmarked our approach on numerous datasets and showed that the consensus genome of samples could be obtained reliably without further manual data curation. Our pipeline can be a valuable tool for fast identifying viral samples. The pipeline is publicly available on the project’s GitHub page (https://github.com/laczkol/QVG).

show abstract

Section: Plos Onesupporting

confidence: 90%

Section: Plos Onementioning

confidence: 99%

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data

et al. 2022

View full text Add to dashboard Cite

show abstract

“…Eight of the 10 AF1b lineages have only been seen in Tanzania, while the remainder have been detected in multiple countries ( S1 Table ). This subclade has good definition due to the large number of sequences, with over 10% of these WGS from a large South African study [ 31 ] and several studies in Tanzania [ 10 , 28 , 39 ] that generated over 80% of the available AF1b WGS. When incorporating N gene data for AF1b, the limited diversity compared to WGS means additional N gene sequences do not translate into designated lineages, as also evident in the ME1a and WE subclades ( Fig 4 and Table 1 ).…”

Section: Discussionmentioning

confidence: 99%

Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination

et al. 2022

View full text Add to dashboard Cite

The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 96 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, as well as areas of persistence and routes of virus movement, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as countries work towards eliminating dog-mediated rabies, as well as having potential for broader application to the surveillance of other viruses.

show abstract

“…To demonstrate that our approach can process not only AmpliSeq datasets, we run the Rabies virus (RABV) dataset presented by Sabeta et al (2020) [20] through our pipeline. Sequencing reads of this dataset were obtained after the depletion of host DNA and RNA [20]. To genotype the samples of this dataset, we used the genome of Rabies virus (isolate 20034) (KT336433).…”

Section: Benchmarkingmentioning

confidence: 99%

Rapid genotyping of viral samples using Illumina short-read sequencing data

Váradi

Kaszab

Kardos

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

Complete Coding Sequences of 23 South African Domestic and Wildlife Rabies Viruses

Cited by 4 publications

References 6 publications

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data

Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination

Rapid genotyping of viral samples using Illumina short-read sequencing data

Contact Info

Product

Resources

About