Product Info

The NxSeq™ SARS-CoV-2 Whole Genome Library Kit supplies the targeting primers, enzymes and other reagents necessary to build overlapping, targeted amplicon libraries covering the SARS-CoV-2 genome. These libraries enable whole genome viral sequencing on Illumina instruments for the identification and tracking of SARS-CoV-2 variants. We designed the targeting primer pairs against the Wuhan-Hu-1 strain (NC_045512.2) and carefully screened and optimised the primer set to produce high on-target rates and consistent amplicon yields in order to maximise multiplexing, streamline analysis and keep costs low. Each amplicon target region* overlaps with the target regions of adjacent amplicons in order to generate nearly full coverage and effective variant analysis of each SARS-CoV-2 isolate.

  • Identify both known and novel variants: 98% SARS-CoV-2 genome coverage
  • Fast, easily automated protocol: 2 hours from cDNA to final library with minimal steps
  • Extensive compatibility across Illumina sequencers: Small amplicons enable 2 x 150 PE sequencing chemistry available on more Illumina platforms (compared to amplicon panels >350 bp in size, e.g. ARTIC)
  • High multiplexing drives down costs: 1440 CDI indexes plus uniform coverage maximise multiplexing capabilities and simplify analysis.

Key features

Feature Details
Input Single-stranded or double-stranded cDNA made from positive RNA samples
SARS-CoV-2 genome coverage 98% or 29,355 / 29,903 total nucleotides of viral RNA genome
Amplicon number 341 overlapping amplicons
Amplicon sizes 101 nt average target region* length making it compatible with common 2x150 PE sequencing chemistry
Protocol time 2 hours from cDNA to final library
Components provided** SARS-CoV-2 targeting primers, PCR and library prep components
Index style 15 Indexing plates are available, each with 96 different combinatorial dual indexes
Multiplexing levels Up to 1440 samples when using all 15 different indexing plates
Recommended sequencing depth ~1 million reads per library – may be reduced depending on sample quality

*Target region refers to the portion of each amplicon between the 3’ ends of each forward and reverse primer pair. This portion of each amplicon will provide the useable variant information, and each target region overlaps with an adjacent target region.
** cDNA synthesis reagents and clean-up/size selection beads are not included.

Simple and robust 2 hour protocol from cDNA to final library

This figure illustrates the basic library preparation method used in this targeted amplicon-seq protocol

Figure 1. Overview of the NxSeq SARS-CoV-2 Whole Genome Library Kit protocol. This figure illustrates the basic library preparation method used in this targeted amplicon-seq protocol. In total, there are 341 overlapping library amplicons constructed, and in some cases, the forward and reverse primers from adjacent amplicons may produce longer amplicons that span from the 5’ end of the first amplicon to the 3’ end of the downstream adjacent amplicon. Please note that since the final library is not PCR amplified, there will be some fragments in the library that do not have adaptors at both ends and are not sequenceable (not shown).

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Product Size Cat. No.
NxSeq SARS-CoV-2 Whole Genome Library Kit 96 reactions GEN-SCV2-0096

Each library kit contains SCV2 Targeting Primers, Amplification Primer, PCR Master Mix, Sample Dilution Buffer, Indexing Buffer, Indexing Enzyme 1, 2 and 3, Elution Buffer and PEG/NaCl Solution. At least one indexing plate below must be purchased and used in conjunction with this library preparation kit.

Product Size Cat. No.
Indexing plate 1 96 reactions GEN-9754-001
Indexing plate 2 96 reactions GEN-9754-002
Indexing plate 3 96 reactions GEN-9754-003
Indexing plate 4 96 reactions GEN-9754-004
Indexing plate 5 96 reactions GEN-9754-005
Indexing plate 6 96 reactions GEN-9754-006
Indexing plate 7 96 reactions GEN-9754-007
Indexing plate 8 96 reactions GEN-9754-008
Indexing plate 9 96 reactions GEN-9754-009
Indexing plate 10 96 reactions GEN-9754-010
Indexing plate 11 96 reactions GEN-9754-011
Indexing plate 12 96 reactions GEN-9754-012
Indexing plate 13 96 reactions GEN-9754-013
Indexing plate 14 96 reactions GEN-9754-014
Indexing plate 15 96 reactions GEN-9754-015

Each Indexing Plate contains 96 combinatorial dual indexes (CDI) in an (8) i5 x (12) i7 matrix. See the Indexing Plate layout and indexes Excel file in the Resources section for more details including plate layouts, indexes and sequences per well.

For Research Use Only. Not for use in diagnostic procedures.