Optimization data for an ARTIC-/Illumina-based whole-genome sequencing protocol and pipeline for SARS-CoV-2 analysis

被引：0

作者：

Bundschuh, Christian ^{[1
]}

Weidner, Niklas ^{[1
,2
]}

Klein, Julian ^{[1
]}

Rausch, Tobias ^{[3
]}

Azevedo, Nayara ^{[3
]}

Telzerow, Anja ^{[1
,3
]}

Jost, Katharina Laurence ^{[1
]}

Schnitzler, Paul ^{[1
]}

Kraeusslich, Hans-Georg ^{[1
,4
]}

Benes, Vladimir ^{[3
]}

机构：

[1] Heidelberg Univ, Med Fac Heidelberg, Dept Infect Dis Virol, Heidelberg, Germany

[2] Heidelberg Univ, Med Fac Heidelberg, Dept Infect Dis Microbiol & Hyg, Heidelberg, Germany

[3] European Mol Biol Lab EMBL, Genom Core Facil, Heidelberg, Germany

[4] Deutsch Zentrum Infekt Forsch, Partner Site Heidelberg, Heidelberg, Germany

来源：

DATA IN BRIEF | 2024年 / 55卷

关键词：

Virology; Epidemiology; Whole genome sequencing; Bioinformatics; SARS-CoV-2;

D O I：

10.1016/j.dib.2024.110607

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

In January 2021, Germany commenced surveillance of SARSCoV-2 variants under the Corona Surveillance Act, which ceased in July 2023. The objective was to bolster pandemic control, as specific alterations in amino acids, particularly within the spike protein, were linked to heightened transmission and decreased vaccine effectiveness. Consequently, our team conducted whole genome sequencing using the commercially accessible ARTIC protocol on Illumina's NextSeq50 0 platform and MiSeq for SARS-CoV-2 positive samples obtained from patients at Heidelberg University Hospital, affiliated hospitals, and the public health office in the Rhine-Neckar/Heidelberg region. Throughout the pandemic, we refined the existing ARTIC V4 protocol as well as our bioinformatics pipeline, the details of which are outlined in this report. This report reflects the protocol for the MiSeq analysis, the protocol for the NextSeq50 0 can be found in our previous publication.

引用

页数：13

共 50 条

[41] Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification [J].

Peng, Mengfei ;

Davis, Morgan L. ;

Bentz, Meghan L. ;

Burgin, Alex ;

Burroughs, Mark ;

Padilla, Jasmine ;

Nobles, Sarah ;

Unoarumhi, Yvette ;

Tang, Kevin .

VIRUSES-BASEL, 2025, 17 (04)

[42] PneusPage: A WEB-BASED TOOL for the analysis of Whole-Genome Sequencing Data of Streptococcus pneumonia [J].

Hong, Eunju ;

Shin, Youngjin ;

Kim, Hyunseong ;

Cho, Woo Young ;

Song, Woo-Hyun ;

Jung, Seung-Hyun ;

Lee, Minho .

JOURNAL OF MICROBIOLOGY, 2025, 63 (01) :e.2409020

[43] A Rapid, Whole Genome Sequencing Assay for Detection and Characterization of Novel Coronavirus (SARS-CoV-2) Clinical Specimens Using Nanopore Sequencing [J].

Arevalo, Maria T. ;

Karavis, Mark A. ;

Katoski, Sarah E. ;

Harris, Jacquelyn V. ;

Hill, Jessica M. ;

Deshpande, Samir V. ;

Roth, Pierce A. ;

Liem, Alvin T. ;

Bernhards, R. Cory .

FRONTIERS IN MICROBIOLOGY, 2022, 13

[44] Impact of cobas PCR Media freezing on SARS-CoV-2 viral RNA integrity and whole genome sequencing analyses [J].

Benoit, Patrick ;

Point, Floriane ;

Gagnon, Simon ;

Kaufmann, Daniel E. ;

Tremblay, Cecile ;

Harrigan, Richard Paul ;

Hardy, Isabelle ;

Coutlee, Francois ;

Lapierre, Simon Grandjean .

DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE, 2021, 101 (04)

[45] Use of whole genome sequencing to identify low-frequency mutations in SARS-CoV-2 patients treated with remdesivir [J].

Nirmalarajah, Kuganya ;

Yim, Winfield ;

Aftanas, Patryk ;

Li, Angel X. ;

Shigayeva, Altynay ;

Yip, Lily ;

Zhong, Zoe ;

Mcgeer, Allison J. ;

Maguire, Finlay ;

Mubareka, Samira ;

Kozak, Robert .

INFLUENZA AND OTHER RESPIRATORY VIRUSES, 2023, 17 (09)

[46] Molecular Characterization of Whole-Genome SARS-CoV-2 from the First Suspected Cases of the XE Variant in the Lazio Region, Italy [J].

Rueca, Martina ;

Giombini, Emanuela ;

Gramigna, Giulia ;

Gruber, Cesare Ernesto Maria ;

Fabeni, Lavinia ;

Corpolongo, Angela ;

Mazzotta, Valentina ;

Corso, Luisella ;

Butera, Ornella ;

Valli, Maria Beatrice ;

Carletti, Fabrizio ;

Pignalosa, Stefano ;

Vairo, Francesco ;

Nicastri, Emanuele ;

Antinori, Andrea ;

Girardi, Enrico ;

Vaia, Francesco ;

Maggi, Fabrizio .

DIAGNOSTICS, 2022, 12 (09)

[47] An optimized, amplicon-based approach for sequencing of SARS-CoV-2 from patient samples using COVIDSeq assay on Illumina MiSeq sequencing platforms [J].

Bhoyar, Rahul C. ;

Senthivel, Vigneshwar ;

Jolly, Bani ;

Imran, Mohamed ;

Jain, Abhinav ;

Divakar, Mohit Kumar ;

Scaria, Vinod ;

Sivasubbu, Sridhar .

STAR PROTOCOLS, 2021, 2 (03)

[48] Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa [J].

Fares, Wasfi ;

Chouikha, Anissa ;

Ghedira, Kais ;

Gdoura, Meriam ;

Rezig, Dorra ;

Boubaker, Sondes Haddad ;

Dhifallah, Imen Ben ;

Touzi, Henda ;

Hammami, Walid ;

Meddeb, Zina ;

Sadraoui, Amel ;

Hogga, Nahed ;

Abouda, Imen ;

Kwasiborski, Aurelia ;

Hourdel, Veronique ;

Mikaty, Guillain ;

Caro, Valerie ;

Manuguerra, Jean-Claude ;

Alaya, Nissaf Ben ;

Triki, Henda .

BMC GENOMICS, 2021, 22 (01)

[49] Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa [J].

Wasfi Fares ;

Anissa Chouikha ;

Kais Ghedira ;

Meriam Gdoura ;

Dorra Rezig ;

Sondes Haddad Boubaker ;

Imen Ben Dhifallah ;

Henda Touzi ;

Walid Hammami ;

Zina Meddeb ;

Amel Sadraoui ;

Nahed Hogga ;

Imen Abouda ;

Aurélia Kwasiborski ;

Véronique Hourdel ;

Guillain Mikaty ;

Valérie Caro ;

Jean-Claude Manuguerra ;

Nissaf Ben Alaya ;

Henda Triki .

BMC Genomics, 22

[50] First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia [J].

Vidanovic, Dejan ;

Tesovic, Bojana ;

Volkening, Jeremy D. ;

Afonso, Claudio L. ;

Quick, Joshua ;

Sekler, Milanko ;

Knezevic, Aleksandra ;

Jankovic, Marko ;

Jovanovic, Tanja ;

Petrovic, Tamas ;

Deri, Bojana Banovic .

EPIDEMIOLOGY & INFECTION, 2021, 149

← 1 2 3 4 5 →