Next Article in Journal
The gp44 Ejection Protein of Staphylococcus aureus Bacteriophage 80α Binds to the Ends of the Genome and Protects It from Degradation
Next Article in Special Issue
Zika Virus in West Africa: A Seroepidemiological Study between 2007 and 2012
Previous Article in Journal / Special Issue
West Nile Virus Lineage 2 Vector Competence of Indigenous Culex and Aedes Mosquitoes from Germany at Temperate Climate Conditions

Evaluation of Viral RNA Recovery Methods in Vectors by Metagenomic Sequencing

Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Austrasse, CH-3700 Spiez, Switzerland
Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland
Graduate School for Cellular and Biomedical Sciences, University of Bern, Hochschulstrasse 4, 3012 Bern, Switzerland
Authors to whom correspondence should be addressed.
Viruses 2020, 12(5), 562;
Received: 29 April 2020 / Revised: 17 May 2020 / Accepted: 18 May 2020 / Published: 19 May 2020
(This article belongs to the Special Issue Emerging Arboviruses)
Identification and characterization of viral genomes in vectors including ticks and mosquitoes positive for pathogens of great public health concern using metagenomic next generation sequencing (mNGS) has challenges. One such challenge is the ability to efficiently recover viral RNA which is typically dependent on sample processing. We evaluated the quantitative effect of six different extraction methods in recovering viral RNA in vectors using negative tick homogenates spiked with serial dilutions of tick-borne encephalitis virus (TBEV) and surrogate Langat virus (LGTV). Evaluation was performed using qPCR and mNGS. Sensitivity and proof of concept of optimal method was tested using naturally positive TBEV tick homogenates and positive dengue, chikungunya, and Zika virus mosquito homogenates. The amount of observed viral genome copies, percentage of mapped reads, and genome coverage varied among different extractions methods. The developed Method 5 gave a 120.8-, 46-, 2.5-, 22.4-, and 9.9-fold increase in the number of viral reads mapping to the expected pathogen in comparison to Method 1, 2, 3, 4, and 6, respectively. Our developed Method 5 termed ROVIV (Recovery of Viruses in Vectors) greatly improved viral RNA recovery and identification in vectors using mNGS. Therefore, it may be a more sensitive method for use in arbovirus surveillance. View Full-Text
Keywords: vector-borne viruses; vectors; sample processing; NGS; metagenomics vector-borne viruses; vectors; sample processing; NGS; metagenomics
Show Figures

Figure 1

MDPI and ACS Style

Akello, J.O.; Leib, S.L.; Engler, O.; Beuret, C. Evaluation of Viral RNA Recovery Methods in Vectors by Metagenomic Sequencing. Viruses 2020, 12, 562.

AMA Style

Akello JO, Leib SL, Engler O, Beuret C. Evaluation of Viral RNA Recovery Methods in Vectors by Metagenomic Sequencing. Viruses. 2020; 12(5):562.

Chicago/Turabian Style

Akello, Joyce O., Stephen L. Leib, Olivier Engler, and Christian Beuret. 2020. "Evaluation of Viral RNA Recovery Methods in Vectors by Metagenomic Sequencing" Viruses 12, no. 5: 562.

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

Back to TopTop