Nijmegen, The Netherlands, March 29, 2021
Following the release and success of their EasySeq™ SARS-CoV-2 WGS kit in 2020, NimaGen BV announce the further expansion of their kit range to facilitate higher throughput application of SARS-CoV-2 Whole Genome Sequencing (WGS) with the launch of a 384-sample version kit for Illumina sequencing and the addition of an expanded selection of accompanying Unique Dual Indexes (UDIs) now increased to 1536 UDIs.
Rapid and Simplified Library Preparation for viral surveillance
The recent emergence and spread of new nCoV-2 variants have clearly demonstrated the importance and need for rapid and high throughput screening for SARS-CoV-2 for viral surveillance.
Utilising Reverse Complement PCR (RC-PCR), WGS library preparation with the EasySeq™ SARS-CoV-2 kit could not be simpler- with just a single PCR reaction for both Amplicon generation and indexing.
Assay set-up is extremely easy and ideally suited for automation, with just 2 dispensing steps of sample and Mastermix to pre-spotted index plates before loading in the Thermocycler.
Following the single PCR all samples can immediately be pooled for a single-tube magnetic bead clean-up step and once standard quality control checks have been performed the library is ready for sequencing. This drastically simplified protocol can reduce hands on time for library prep by up to 80% compared with other methods currently being used for the WGS of SARS-CoV-2.
Dr. Josh Quick from the Institute of Microbiology & Infection, University of Birmingham, UK and who was integrally involved in the creation of the ARTIC Network SARS-CoV-2 sequencing protocol has commented:
"Multiplex RC-PCR is one of the solutions emerging from the pandemic that has excited me the most. The approach combines the robustness of amplicon sequencing with the scalability of PCR barcoding in a single PCR step, something I have puzzled over for years. In our testing the sensitivity was comparable to other amplicon based methods but with a greatly streamlined Illumina library preparation workflow and I am optimistic that there is even more performance to come with this approach in future."
Simpler and more rapid library prep does allow for more samples to be prepared each day, improving public health authority’s ability to monitor the epidemic and the emergence, and spread of new variants.
Sequence every positive COVID-19 Sample?
“The addition of a 384 well version of the kit to the range will certainly help our high-throughput customers streamline their library preparation even further” says Joop Theelen, CSO and co-founder of NimaGen “Also, with up to 1536 accompanying UDIs now available, more than 3000 SARS-CoV-2 whole genomes could be sequenced on one Illumina NovaSeq SP dual lane flowcell – bringing the possibility to sequence every positive COVID-19 sample closer than ever before.”
NimaGen are also rapidly developing a “one-step” version of the kit that works direct on RNA samples, thus avoiding the need for a separate cDNA synthesis reaction before WGS library preparation.
By adapting the RC-PCR method, cDNA synthesis, amplification and indexing can be carried out in a single closed tube PCR reaction, further streamlining the complete workflow, and allowing for increased throughput.
“The need for a separate cDNA synthesis step is currently a potential major workflow bottleneck for our customers and as with any additional handling step it also adds to the risks around assay and sample security” Walter van der Vliet, NGS Application & Development Scientist at NimaGen says “If we can incorporate the generation of cDNA into the RC-PCR reaction then our customers can go direct from extracted RNA to indexed amplicons in just one PCR step, making the whole workflow faster and more secure and ultimately allowing them to process more samples each day”
Early development data looks positive and NimaGen expects to have the product commercially available in spring 2021.
Further details available at www.nimagen.com/covid19