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Illumina Microbial Amplicon Prep

A flexible and streamlined NGS library prep kit that enables various public health surveillance and microbial research applications.

< 9 hr

Assay time

~3 hr for 48 samples

Hands-on time

Varies depending on sample source

Input quantity

See full details in the specifications table

Overview

Illumina Microbial Amplicon Prep (iMAP) is an amplicon-based library preparation kit built on the same chemistry as COVIDSeq. Library preparation is fast and simple, with libraries compatible with nearly all Illumina sequencing systems. It can be used for various infectious disease, public health surveillance, and microbial research applications, including viral whole-genome sequencing, antimicrobial resistance marker analysis, bacterial and fungal identification, and more.

Expand your microbial research capabilities

Get sequencing results with exceptional data quality and accuracy at any scale with low hands-on time.

  • Target variants with ready-to-use or lab-designed oligos

  • Use a multiplexed, PCR-based workflow

  • Interpret data with simple analysis solutions

  • Sequence a broad range of samples

The kit can be used with custom, published, or commercially available primer sets (primer oligos are not included) and is compatible with RNA or DNA extracted from sources such as cultures, swabs (nasopharyngeal, skin, and nasal), wastewater, and more. Analysis can be performed using the DRAGEN Targeted Microbial App on Basespace Sequence Hub with pre-loaded targets. Files can also be easily uploaded for custom analyses.

Illumina tested protocols
  • Chikungunya1
  • Dengue1
  • Mpox1
  • RSV1
  • Zika1
Customer demonstrated protocols*

*Protocols provided for informational purposes only. This does not imply the protocols are validated or supported by Illumina.

 

References

1. Illumina. Accessed September 8, 2023, from Illumina Microbial Amplicon Prep for viral surveillance

2. DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus V.2. Accessed September 8, 2023, from https://www.protocols.io/view/dengueseq-a-pan-serotype-whole-genome-amplicon-seq-kqdg39xxeg25/v2

3. Bhatt L, Bhoyar RC, Jolly B, Israni R, Vignesh H, Scaria V, Sivasubbu S. The genome sequence of lumpy skin disease virus from an outbreak in India suggests a distinct lineage of the virus. Arch Virol. 2023 Feb 5;168(3):81. doi: 10.1007/s00705-023-05705-w.

4. Monkeypox virus multiplexed PCR amplicon sequencing (PrimalSeq) V.4. Accessed September 8, 2023, from https://www.protocols.io/view/monkeypox-virus-multiplexed-pcr-amplicon-sequencin-5qpvob1nbl4o/v4?step=2

5. Whole-Genome Amplification of Respiratory Syncytial Virus (RSV) using Illumina CovidSeq reagents for Next-Generation Sequencing V.2. Accessed September 8, 2023, from https://www.protocols.io/view/whole-genome-amplification-of-respiratory-syncytia-eq2lyjzbrlx9/v2

6. SARS-CoV-2 version 5.3.2 scheme release. Accessed September 12, 2023, from https://community.artic.network/t/sars-cov-2-version-5-3-2-scheme-release/462

7. Rabies Virus Bat-Clade Sequencing. Accessed October 30, 2023, from https://www.protocols.io/view/rabies-virus-bat-clade-sequencing-8epv5x3bng1b/v1

Specifications

Assay time < 9 hr
Automation capability Liquid handling robots
Description Illumina Microbial Amplicon Prep (IMAP) is an amplicon-based library preparation solution that includes RT-PCR, library prep, and indexes for 48 samples. It is built on the same chemistry as COVIDSeq and can be used with DNA and RNA samples. Oligo primers are not provided in the kit and are sourced separately.
Hands-on time ~3 hr for 48 samples
Input quantity Varies depending on sample source
Instruments MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiSeqDx in Research Mode, MiniSeq System, NextSeq 550Dx in Research Mode, NovaSeq 6000Dx in Research Mode, NovaSeq 6000 System
Mechanism of action Multiplex PCR
Method Amplicon sequencing
Nucleic acid type DNA, RNA
Sample type details Works with a wide variety of sample types from nasal swabs to wastewater
Species category Other, Yeast, Virus, Bacteria
Technology Sequencing
Variant class Single nucleotide polymorphisms (SNPs), Single nucleotide variants (SNVs)

Applications

Example workflow

1
Prep

Illumina Microbial Amplicon Prep

2
Sequence
3
Analyze

Related applications and methods

Wastewater surveillance

Learn about wastewater surveillance with NGS for community-level monitoring of infectious diseases, mutation tracking, and variant trend tracking.

Genomic surveillance of infectious diseases

NGS supports effective genomic surveillance strategies through identification of novel strains of coronavirus and other emerging infectious disease agents.

Amplicon sequencing

Ultra-deep sequencing of PCR amplicons enables analysis of specific genomic regions of interest. Learn more about amplicon sequencing and find comprehensive solutions.

Documentation

Product literature
Support documentation

Resources

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Fast, flexible library prep with IMAP

In this video, Illumina Scientist Jeff Koble provides an overview of the Illumina Microbial Amplicon Prep assay, detailing tips and tricks to help ensure successful preparation of libraries.

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Simple and efficient IMAP analysis with DRAGEN Targeted Microbial App

Illumina Bioinformatics Scientist Soo Bin Kwon demonstrates how DRAGEN Target Microbial enables comprehensive analysis of microbial targets sequenced with IMAP.

Illumina Microbial Amplicon Prep

20097857

48-sample amplicon kit containing cDNA conversion, library prep, and indexes. Primers are not included.

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