Full length genomes from only 1,000 copies of SARS-CoV-2 RNA
SARS-CoV-2 is encoded by a positive-sense, single-stranded RNA molecule that can be mixed with host RNA during isolation from a sample. The service includes reverse transcription of the RNA into cDNA, enrichment of the viral genome by using an improved primer set - similar to the ARTIC primers - (consisting of over 200 primer pairs, covering the full 29.9 kb viral genome), generation of high quality libraries and sequencing.
++ Information: Our improved primer set is working with all variants - including Omikron ++
- Sequencing service to support real-time genomic infectious disease epidemiology
- Phylogeny and surveillance studies
- Virus variant identification and antigen evolution tracking for vaccine development
- Corona research projects
- Waste water testing --> all details under tab "Waste water"
Highlights of the ARTIC SARS-CoV2 Total RNA sequencing product
- Sequencing of the complete full 29.9 kb viral ssRNA genome
- Depending on viral load on average 0.5 M read pairs
- Processing of any number of samples, starting with one sample
- Preparation of cDNA, enrichment of the viral genome by using proprietary primers and library preparation
- Sequencing with 2x150 bp read mode and on average output of on average 1M read pairs (2x 150 bp)
- Trimming of primers, mapping on SARS-CoV-2 reference; SNP table, alignment-based consensus virus genome sequence generation for samples with a genome coverage > 90%
- Available under ISO 17025 accreditation
- Optimal for positive samples with significant viral loads to ensure full genome coverage. Usually RT-PCR positive samples with Ct value below 30 enable full-length viral genome sequences
Learn more about the SARS-CoV 2 Full-length Genome Sequencing product
Accepted starting material
- Total RNA from various sources (including swabs)
- DNAse-free RNA
- Quantity: Based on SARS-CoV-2 qRT-PCR testing, the Ct value between 18–30. Dilute highly concentrated samples in RNase-free water, as follows: Ct value 12–15, dilute 100-fold; Ct value 16–18, then dilute 10-fold. This will also reduce the likelihood of PCR-inhibition.
- Purity: OD 260/280: 1.8 - 2.0; OD 260/230: 2.0 - 2.2; RIN or RQI value ≥ 8
- Volume: 20µl
Details for waste water samples can be found in the next tab
ARTIC SARS-CoV-2 RNA library
- 150 bp paired-end reads
- Up to 0,5 M read pairs - depending on the viral load
- Sequence cleaning to remove adapters and poor quality bases
- Mapping of high quality sequencing reads to reference SARS-CoV-2 genome
- Identification of SARS-CoV-2 positive samples based on genome coverage analysis
- Determination of consensus* SARS-CoV-2 sequence of the isolate
*Consensus sequence is determined for isolate samples with sufficient coverage (>3x minimum coverage of >95% of the SARS-CoV-2 genome)
- Fastq raw data (avg 1.0 M reads, 2x150 Illumina reads to yield sufficient viral genome coverage)
- Full-length viral consensus genome sequence and variant calling (for samples yielding 90% genome coverage with at least 15-30x for each individual base)
- Bioinformatics analysis and report including comprehensive variant table, Pangolin code (e.g. B.1.1.7 for the UK variant), coverage plots, key quality metrics, etc
- All accessible for download from our secure FTP server.
It is not possible to perform a sample entry QC on these samples. If the final QC prior sequencing fails, we will not sequence your samples (only library prep will be invoiced).
Waste water testing
Eurofins Genomics optimised workflow for SARS-CoV-2 detection can also be used using waste water samples.
Waste water testing is an optimal solution to analyse the SARS-CoV-2 distribution within a population.
Full coverage of the Spike (s) gene of SARS-CoV-2
The service includes reverse transcription of the RNA into cDNA, enrichment of the Spike (s) gene of SARS-Cov-2 by using an improved primer set - similar to the ARTIC primers - (covering the full 3.822 kb S-gene), generation of high quality libraries and sequencing.
crAssphage and pepper mild mottle virus are co-detected as indicators of presence human feces.
Internal spike-in controls monitor presence of PCR inhibitors to avoid false-negative findings. Our improved primer set is working with all variants - including Omikron.
Designed for waste water samples with low viral loads to ensure full S-gene coverage. Usually qPCR positive samples with Ct value below 36 enable full-length S-gene sequences.
The pipeline was further optimized to identify mixed populations of Sars-CoV-2 variants of concern (VOC).
The SARS-CoV-2 Surveillance Report includes comprehensive reporting of SARS-CoV-2 status (including presence of human feces and detection of PCR inhibitors), mutation tables, Pangolin code, coverage plots and key quality metrics. For mixed VOC populations SARS-CoV-2, the proportion of each VOC is indicated.
- Total RNA from various sources
- DNAse-free RNA
- Ct value < 36
- Volume: 20µl