Detection of SARS-CoV-2 from clinical samples
Given its huge capacity, massively parallel sequencing of viral genomes is a powerful tool for the studies of emerging infectious diseases. It can be used for tracing the outbreak origin and drivers as well as transmission chains, mapping the spread and monitoring the evolution of the causing agents.
We have implemented two different NGS techniques suitable for the direct assessment of clinical samples with low virus abundance, such as nasal swabs, to help and support researchers and healthcare professionals in the fight against COVID-19.
Methods are universal and can be adopted to examine any virus sequence of any organism.
We are applying direct amplification of the virus using tiled multiple primers based on the ARTIC protocol. The method is highly sensitive and widely adopted for SNP identification of low titer samples. It is the fastest and the most economical way to understand the epidemiology and evolution of the virus in large cohorts.
The approach is not recommended for the sequencing of highly diverse or recombinant viruses because the primers are specific to known viral genomes.
This high-throughput sequencing method identifies and genotypes all microbial communities in a sample without prior knowledge of what microbes are present. Given its non-discriminating nature it is the best choice when novel pathogens are to be identified. In addition to target viral genome, shotgun approach allows to investigate RNA expression patterns of the overall microbiome as well as host content. Thus, it is suitable for discovering new viruses, distinguishing co-infections, and dissecting virus-host interactions. All this information is valuable not only for the tracking of the virus mutational history and spread patterns but also for informing future treatment decisions and predicting patient outcomes.
Our standard service will include a dedicated analysis pipeline for the reporting of a consensus sequence with a minimum coverage of 5X. For RNA-Seq data, taxonomical classification and relative abundance of bacterial, viral and fungal microorganisms will be reported.
Discover how we obtained genomic information from SARS-Cov-2 genomes directly from clinical samples with virtually non-detectable amounts of RNA. Read more here.