20097857, Illumina Microbial Amplicon Prep

Name: Illumina Microbial Amplicon Prep
Brand: Illumina
SKU: 20097857

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

Catalog Number: 20097857

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NGS Library Preparation Kits

TagsSequencing kits Library preparation kits

Description

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.
Chikungunya 1
Dengue 1
Mpox 1
RSV 1
Zika 1
Chikungunya Virus 2 ( https://www.sciencedirect.com/science/article/pii/S1876034124001394?via%3Dihub )
Dengue I - IV 3 ( https://www.protocols.io/view/dengueseq-a-pan-serotype-whole-genome-amplicon-seq-kqdg39xxeg25/v3 )
Oropouche Virus 4 ( https://www.nature.com/articles/s41591-024-03300-3 )
Powassan Virus 5 ( https://wwwnc.cdc.gov/eid/article/29/2/22-0410_article )
Mpox Virus 6 ( https://www.protocols.io/view/monkeypox-virus-multiplexed-pcr-amplicon-sequencin-5qpvob1nbl4o/v4?step=2 )
RSV: Maloney 7 ( https://www.protocols.io/view/rsv-illumina-whole-genome-sequencing-8epv5rbnng1b/v1 )
RSV: Spain 8 ( https://www.protocols.io/view/whole-genome-amplification-of-respiratory-syncytia-eq2lyjzbrlx9/v3 )
SARS-CoV-2 (ARTIC v5.4.2) 9 ( https://community.artic.network/t/scheme-release-artic-sars-cov2-400-v5-4-2/546 )
Human bocavirus 10 ( https://doi.org/10.1002/jmv.29706 )
Hepatitis A Virus 11 ( https://www.medrxiv.org/content/10.1101/2024.05.05.24306642v1 )
Lumpy Skin Disease Virus 12 ( https://doi.org/10.1016/j.xpro.2024.103020 )
Enterobacter cloacae complex 13 ( https://doi.org/10.3389/fcimb.2022.951049 )
Enterobacter hormaechei 14 ( https://doi.org/10.3390/genes15060814 )
Rabies 15 (protocols.io/view/rabies-virus-bat-clade-sequencing-8epv5x3bng1b/v1)
Western Equine Encephalitis 16 ( https://www.nature.com/articles/s44298-024-00078-6 )
HIV-1 ( https://www.protocols.io/view/an-ngs-amplicon-tiling-protocol-for-hiv-1-drug-res-n92ldmq4ol5b/v3 )
Mycobacterium tuberculosis ( https://www.biorxiv.org/content/10.1101/2024.12.19.629550v1 )
Streptococcus pneumoniae ( https://www.biorxiv.org/content/10.1101/2024.12.19.629550v1 )
Highly Pathogenic Avian Influenza A (H5N1) clade 2.3.4.4b 17 ( https://doi.org/10.3201/eid3010.240583 )
Cryptococcus neoformans/gattii 18 ( https://doi.org/10.1093/mmy/myae126 )
Histoplasma capsulatum 18 ( https://doi.org/10.1093/mmy/myae126 )
Human adenovirus 19 ( https://doi.org/10.3389/fviro.2024.1462907 )
Human coronavirus HKU1 20 ( https://doi.org/10.1002/jmv.70217 )
Leptospira spp 21 ( https://doi.org/10.1016/j.ijmmb.2025.100813 )
*Protocols provided for informational purposes only. This does not imply the protocols are validated or supported by Illumina.

Example workflow
Illumina Microbial Amplicon Prep
iSeq 100 System
MiniSeq System
MiSeq System
NextSeq 550 System
NextSeq 1000 and 2000 Systems
DRAGEN Microbial Amplicon App

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.

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.

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.

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. View less
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Illumina. Accessed September 8, 2023, from Illumina Microbial Amplicon Prep for viral surveillance
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
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
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
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
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
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
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
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
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
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
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.
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
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
Godinho FMS, Campos A, Huff R, et al. 2025. Development and validation of an all-in-one rabies virus Bat-Clade genomic sequencing and host identification protocol. J Virol Methods. 333:115097.
Tomás G, Marandino A, Rodríguez S. et al. 2024. Diagnosis and genomic characterization of the largest western equine encephalitis virus outbreak in Uruguay during 2023–2024. npj Viruses 2, 70
Kim I, Nam J, Kim C, Choi Y, Lee H, An B, et al. Pathogenicity of Highly Pathogenic Avian Influenza A(H5N1) Viruses Isolated from Cats in Mice and Ferrets, South Korea, 2023. Emerg Infect Dis. 2024;30(10):2033-2041.
Trecourt A, Rabodonirina M, Donzel M, et al. 2025. Cryptococcus neoformans/g attii and Histoplasma capsulatum var. capsulatum infections on tissue sections: Diagnostic pitfalls and relevance of an integrated histomolecular diagnosis. Medical Mycology 63, myae126
Nath R, Choudhury G, Gogoi A, et al. 2024. Molecular characterization of human adenovirus associated with pediatric severe acute respiratory infections in a tertiary care hospital in North East India. Front. Virol. 4:1462907.
Hikmat H, Le Targa L, Boschi C, et al. 2025. Five‐Year (2017–2022) Evolutionary Dynamics of HumanCoronavirus HKU1 in Southern France With Emergenceof Viruses Harboring Spike H512R Substitution. J Med Virol 97:e70217
Gurung S, Tewari D, Sherpa U, Chhophel TP, Siddique AI, Sarmah N, Borkakoty B. Fatal case of Leptospira wolffii infection in Sikkim, India: An autochthonous case from a new geographical region. Indian J Med Microbiol. 2025 Feb 25;54:100813. doi: 10.1016/j.ijmmb.2025.100813. Epub ahead of print. PMID: 39986467.

Specifications

General

Assay time	< 9 hr
Hands-on time	~3 hr for 48 samples
Input quantity	Varies depending on sample source
Automation capability	Liquid handling robot(s)
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.
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 , MiSeq i100 System , MiSeq i100 Plus 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)

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