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Updated: Dec 12, 2025

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

Published on: June 25, 2017

De novo sequence assembly requires bioinformatic checking of chimeric sequences.

Laila Sara Arroyo Mühr¹, Camilla Lagheden¹, Sadaf Sakina Hassan¹

¹Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.

|August 11, 2020

Summary

Chimeric sequences, combining viral and non-viral DNA, can lead to false virus detection in sequencing. A new script helps identify these Human Papillomavirus (HPV) chimeras to ensure accurate results.

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Identification of Functional Protein Regions Through Chimeric Protein Construction

Identification of Functional Protein Regions Through Chimeric Protein Construction

Published on: January 8, 2019

Area of Science:

Genomics
Bioinformatics
Virology

Background:

De novo assembly of next-generation sequencing data is crucial for viral detection in biospecimens.
Amplification artifacts and complex viral populations can generate erroneous chimeric sequences.
Chimeras can also form between viral and non-viral sequences, leading to misidentification of viruses.

Purpose of the Study:

To investigate the occurrence and impact of chimeric sequences in viral detection.
To highlight the necessity of chimera checking in bioinformatics pipelines.
To develop a method for identifying Human Papillomavirus (HPV) chimeric sequences.

Main Methods:

Analysis of metagenomic sequencing data from non-melanoma skin cancers (NMSCs) using Illumina NextSeq.
Alignment of high-quality reads against a Human Papillomavirus (HPV) database.
Development of a novel script to identify HPV chimeric sequences.

Main Results:

HPV sequences were detected in 9 out of 91 NMSC specimens via read alignment.
A previous de novo assembly analysis reported 3 additional HPV-positive specimens.
Discrepancies were primarily attributed to chimeric sequences containing both viral and non-viral components.

Conclusions:

Chimeric sequences, including viral-non-viral hybrids, can cause erroneous virus detection.
Implementing chimera checking is essential for accurate viral identification in sequencing data.
A novel script was developed to specifically detect HPV chimeric sequences, improving diagnostic accuracy.