Evaluation of a custom designed hybridisation assay for whole genome sequencing of human adenoviruses direct from clinical samples
Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved..
BACKGROUND: Human Adenoviruses are a common cause of disease and can cause significant morbidity and mortality in immunocompromised patients. Nosocomial transmission events can occur with whole genome sequencing playing a crucial role. This study evaluates the performance of a custom designed SureSelectXT target enrichment assay based on 14 adenovirus genomes for sequencing direct from clinical samples.
METHODS: Modifications were made to the SureSelectXT low input protocol to enhance performance for viral targets. Consensus sequences were generated using an in-house designed three stage bioinformatics pipeline. We assessed, percentage of on target reads, average depth of coverage and percentage genome coverage to determine assay performance across a range of sample matrices.
RESULTS: Whole genome sequences were successfully generated for 91.6 % of samples assessed. Adenovirus DNA concentration was a good indicator of enrichment success. Highly specific enrichment was observed with only 6 % of samples showing < 50 % on target reads. Respiratory and faecal samples performed well where bloods showed higher levels of non-specific enrichment likely confounded by low adenovirus DNA concentrations. Protocol performance did not appear impacted by Adenovirus type or species.
CONCLUSION: Overall performance of this modified SureSelectXT protocol appears in line with previously published works although there are some confounding factors requiring further investigation. The use of a small RNA bait set has the potential to reduce associated costs which can be prohibitive.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2024 |
|---|---|
| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:171 |
|---|---|
| Enthalten in: |
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology - 171(2024) vom: 15. Apr., Seite 105640 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Davies, Emma Ann [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
63231-63-0 |
|---|
| Anmerkungen: |
Date Completed 18.03.2024 Date Revised 02.04.2024 published: Print-Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1016/j.jcv.2024.105640 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM367102285 |
|---|
| LEADER | 01000caa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM367102285 | ||
| 003 | DE-627 | ||
| 005 | 20240403000051.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 240115s2024 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1016/j.jcv.2024.105640 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1361.xml |
| 035 | |a (DE-627)NLM367102285 | ||
| 035 | |a (NLM)38219683 | ||
| 035 | |a (PII)S1386-6532(24)00002-7 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Davies, Emma Ann |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Evaluation of a custom designed hybridisation assay for whole genome sequencing of human adenoviruses direct from clinical samples |
| 264 | 1 | |c 2024 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 18.03.2024 | ||
| 500 | |a Date Revised 02.04.2024 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved. | ||
| 520 | |a BACKGROUND: Human Adenoviruses are a common cause of disease and can cause significant morbidity and mortality in immunocompromised patients. Nosocomial transmission events can occur with whole genome sequencing playing a crucial role. This study evaluates the performance of a custom designed SureSelectXT target enrichment assay based on 14 adenovirus genomes for sequencing direct from clinical samples | ||
| 520 | |a METHODS: Modifications were made to the SureSelectXT low input protocol to enhance performance for viral targets. Consensus sequences were generated using an in-house designed three stage bioinformatics pipeline. We assessed, percentage of on target reads, average depth of coverage and percentage genome coverage to determine assay performance across a range of sample matrices | ||
| 520 | |a RESULTS: Whole genome sequences were successfully generated for 91.6 % of samples assessed. Adenovirus DNA concentration was a good indicator of enrichment success. Highly specific enrichment was observed with only 6 % of samples showing < 50 % on target reads. Respiratory and faecal samples performed well where bloods showed higher levels of non-specific enrichment likely confounded by low adenovirus DNA concentrations. Protocol performance did not appear impacted by Adenovirus type or species | ||
| 520 | |a CONCLUSION: Overall performance of this modified SureSelectXT protocol appears in line with previously published works although there are some confounding factors requiring further investigation. The use of a small RNA bait set has the potential to reduce associated costs which can be prohibitive | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Adenovirus | |
| 650 | 4 | |a Hybrid capture, Agilent, SureSelect | |
| 650 | 4 | |a Targeted enrichment | |
| 650 | 4 | |a Whole genome sequencing | |
| 650 | 7 | |a RNA |2 NLM | |
| 650 | 7 | |a 63231-63-0 |2 NLM | |
| 650 | 7 | |a DNA |2 NLM | |
| 650 | 7 | |a 9007-49-2 |2 NLM | |
| 700 | 1 | |a Dutton, Laura |e verfasserin |4 aut | |
| 700 | 1 | |a Guiver, Malcolm |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology |d 1997 |g 171(2024) vom: 15. Apr., Seite 105640 |w (DE-627)NLM097223964 |x 1873-5967 |7 nnns |
| 773 | 1 | 8 | |g volume:171 |g year:2024 |g day:15 |g month:04 |g pages:105640 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1016/j.jcv.2024.105640 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 171 |j 2024 |b 15 |c 04 |h 105640 | ||