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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.

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.

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Primer design for the IMAP protocol with PrimalScheme3

Christopher Kent from the University of Birmingham introduces PrimalScheme3 and discusses best practices for primer design to help optimize IMAP experiments.

Illumina Microbial Amplicon Prep

20097857

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

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References
  1. Illumina. Accessed September 8, 2023, from Illumina Microbial Amplicon Prep for viral surveillance
  2. de La Roque, DGL, Santos EV, Policastro LR, et al. 2024. Exploring the Chikungunya virus landscape in a dengue-endemic Brazilian area. Journal of Infection and Public Health 17(7): 102442
  3. Vogels CB, Hill V, Breban MI, et al. 2024. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics. 25(1): 433
  4. Naveca FG, Pires de Almeida TA, Souza V, et al. 2024. Human outbreaks of a novel reassortant Oropouche virus inthe Brazilian Amazon region. Nature Medicine. Epub ahead of print. Accessed 19 Sep 2024 from https://www.nature.com/articles/s41591-024-03300-3.epdf
  5. Charles H, Hassett E, Vogels CBF, Shapley D, Grubaugh ND, Thangamani, S. 2023. Powassan Virus Lineage I in Field-Collected Dermacentor variabilis Ticks, New York, USA. Emerging Infectious Diseases. 29(2): 415-417
  6. Chen NFG, Chaguza C, Gagne L, et al. 2024. Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus. PLOS Biology. 21(6): e3002151
  7. Maloney DM, Fernandes G, Jasim S, et al. 2024. ARTIC RSV amplicon sequencing reveals global RSV genotype dynamics. bioRxiv pre-print. Accessed 17 Sep 2024 from https://www.biorxiv.org/content/10.1101/2024.08.23.609324v3
  8. Davina-Nunez C, Perez-Castro S, Cabrera-Alvargonzalez JJ, Montano-Barrientos J, Godoy-Diz M, Regueiro, B. 2023. The Modification of the Illumina® CovidSeq™ Workflow for RSV Genomic Surveillance: The Genetic Variability of RSV during the 2022–2023 Season in Northwest Spain. International Journal of Molecular Sciences. 24(22): 16055
  9. SARS-CoV-2 version 5.4.2 scheme release. Accessed 17 Sep 2024 from https://community.artic.network/t/scheme-release-artic-sars-cov2-400-v5-4-2/546
  10. Hikmat H, Le Targa L, Boschi C, et al. 2024. Sequencing and characterization of human bocavirus genomes from patients diagnosed in Southern France between 2017 and 2022. Journal of Medical Virology. 96(6): 10.1002/jmv.29706
  11. Sicilia P, Fantilli AC, Cuba F, et al. 2024. Hepatitis A virus whole genome sequencing strategy using NGS/Illumina technology. medRxiv pre-print. Accessed 17 Sep 2024 from https://doi.org/10.1101/2024.05.05.24306642
  12. Bhoyar RC, Jolly B, Vignesh H, Bhatt L, Senthivel V, Israni R, Scaria V, Sivasubbu S. 2024. Protocol for next-generation sequencing of the LSD virus genome using an amplicon-based approach. STAR Protocols. 5(3):103020.
  13. Knecht CA, García AN, Álvarez VE, et al. 2022. Novel insights related to the rise of KPC-producing Enterobacter cloacae complex strains within the nosocomial niche. Frontiers in Cellular and Infection Microbiology. 12:951049
  14. Ferreira CM, Naveca FG, Ferreira GMA, et al. 2024. Whole-Genome Analysis of Extensively Drug-Resistant Enterobacter hormaechei Isolated from a Patient with Non-Hodgkin’s Lymphoma. Genes. 15(6): 814
  15. Rabies Virus Bat-Clade Sequencing. Accessed October 30, 2023, from https://www.protocols.io/view/rabies-virus-bat-clade-sequencing-8epv5x3bng1b/v1

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