I am looking for the best approach based on illumina platform for sequencing sars-cov-2 genomes obtained from clinical samples.
I already found protocols based on metagenomic approaches, but also virus-directed approaches. We are going to sequence hundred of samples. What do you recommend?
Some resources that I found:
https://www.protocols.io/view/sars-cov-2-genome-sequencing-using-long-pooled-amp-befyjbpw
https://github.com/CDCgov/SARS-CoV-2_Sequencing/blob/master/README.md
Have you utilized one of these protocols? What's your experience with them?
https://www.researchgate.net/deref/https%3A%2F%2Fwww.protocols.io%2Fview%2Fsars-cov-2-genome-sequencing-using-long-pooled-amp-befyjbpw
https://www.researchgate.net/deref/https%3A%2F%2Fwww.protocols.io%2Fview%2Fsars-cov-2-genome-sequencing-using-long-pooled-amp-befyjbpw yeah agree
For virus-directed approaches, you can use the Pan-Viral/SARS-CoV-2 Panel designed by Twist Biosciences. Also you can use the Respiratory Virus Oligos Panel from Illumina. You can use a library prep kit of your choice for pre-enrichment library prep, followed by an enrichment process using one of these probe pools.
High-throughput sequencing (HTS) provides the opportunity, once a diagnostic result is obtained, to extract additional information from a virus-containing sample. Hence, it offers advantages over established quantitative amplification technology, such as quantitative PCR, particularly in a public health environment. At this early stage of its clinical application, there have been limited studies comparing HTS performance to that of the more established quantitative PCR technology for direct detection of viruses. In this pilot-scale study, we tested HTS with a range of viruses and sample types routinely encountered in a public health virology laboratory. In comparison with quantitative PCR, our HTS method was able to sensitively (92%) detect all viruses in any sample type with the exception of certain tissues. Moreover, sufficient nucleotide sequence information was obtained to enable genotyping of strains detected, thus providing additional useful epidemiological information. While HTS sensitivity may not yet match that of PCR, the added value through enhanced epidemiological data has considerable potential to enable real-time surveillance of circulating strains so as to facilitate rapid and appropriate response to outbreaks and virus zoonotic spillover events.