Towards Reliable Whole Genome Sequencing for Outbreak Preparedness and Response

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2022 Aug 9

PMID 35945497

Authors

David F Nieuwenhuijse

Anne van der Linden

Robert H G Kohl

Reina S Sikkema

Marion P G Koopmans

Bas B Oude Munnink

Affiliations

Soon will be listed here.

Abstract

Background: To understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of genetic sequences during outbreaks for public health decision making. Here, we explore the use of metagenomic sequencing compared to specific amplicon- and capture-based sequencing, both on the Nanopore and the Illumina platform for generation of whole genomes of Usutu virus, Zika virus, West Nile virus, and Yellow Fever virus.

Results: We show that amplicon-based Nanopore sequencing can be used to rapidly obtain whole genome sequences in samples with a viral load up to Ct 33 and capture-based Illumina is the most sensitive method for initial virus determination.

Conclusions: The choice of sequencing approach and platform is important for laboratories wishing to start whole genome sequencing. Depending on the purpose of genome sequencing the best choice can differ. The insights presented in this work and the shown differences in data characteristics can guide labs to make a well informed choice.

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References

Paz S, Semenza J . Environmental drivers of West Nile fever epidemiology in Europe and Western Asia--a review. Int J Environ Res Public Health. 2013; 10(8):3543-62. PMC: 3774453. DOI: 10.3390/ijerph10083543. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Goldani L . Yellow fever outbreak in Brazil, 2017. Braz J Infect Dis. 2017; 21(2):123-124. PMC: 9427601. DOI: 10.1016/j.bjid.2017.02.004. View

Javelle E, Gautret P, Raoult D . Towards the risk of yellow fever transmission in Europe. Clin Microbiol Infect. 2018; 25(1):10-12. DOI: 10.1016/j.cmi.2018.08.015. View

Arias A, Watson S, Asogun D, Tobin E, Lu J, Phan M . Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. Virus Evol. 2017; 2(1):vew016. PMC: 5499387. DOI: 10.1093/ve/vew016. View

Oude Munnink B, Nieuwenhuijse D, Stein M, OToole A, Haverkate M, Mollers M . Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nat Med. 2020; 26(9):1405-1410. DOI: 10.1038/s41591-020-0997-y. View

Grubaugh N, Faria N, Andersen K, Pybus O . Genomic Insights into Zika Virus Emergence and Spread. Cell. 2018; 172(6):1160-1162. DOI: 10.1016/j.cell.2018.02.027. View

Chen S, Zhou Y, Chen Y, Gu J . fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018; 34(17):i884-i890. PMC: 6129281. DOI: 10.1093/bioinformatics/bty560. View

Lustig Y, Sofer D, Bucris E, Mendelson E . Surveillance and Diagnosis of West Nile Virus in the Face of Flavivirus Cross-Reactivity. Front Microbiol. 2018; 9:2421. PMC: 6194321. DOI: 10.3389/fmicb.2018.02421. View

10.

Oude Munnink B, Worp N, Nieuwenhuijse D, Sikkema R, Haagmans B, Fouchier R . The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology. Nat Med. 2021; 27(9):1518-1524. DOI: 10.1038/s41591-021-01472-w. View

11.

Sikkema R, Schrama M, van den Berg T, Morren J, Munger E, Krol L . Detection of West Nile virus in a common whitethroat () and mosquitoes in the Netherlands, 2020. Euro Surveill. 2020; 25(40). PMC: 7545818. DOI: 10.2807/1560-7917.ES.2020.25.40.2001704. View

12.

Lessler J, Chaisson L, Kucirka L, Bi Q, Grantz K, Salje H . Assessing the global threat from Zika virus. Science. 2016; 353(6300):aaf8160. PMC: 5467639. DOI: 10.1126/science.aaf8160. View

13.

Cadar D, Luhken R, van der Jeugd H, Garigliany M, Ziegler U, Keller M . Widespread activity of multiple lineages of Usutu virus, western Europe, 2016. Euro Surveill. 2017; 22(4). PMC: 5388094. DOI: 10.2807/1560-7917.ES.2017.22.4.30452. View

14.

Li H . Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018; 34(18):3094-3100. PMC: 6137996. DOI: 10.1093/bioinformatics/bty191. View

15.

Faria N, Kraemer M, Hill S, Goes de Jesus J, Aguiar R, Iani F . Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science. 2018; 361(6405):894-899. PMC: 6874500. DOI: 10.1126/science.aat7115. View

16.

Koster J, Rahmann S . Snakemake--a scalable bioinformatics workflow engine. Bioinformatics. 2012; 28(19):2520-2. DOI: 10.1093/bioinformatics/bts480. View

17.

Lanciotti R, Kosoy O, Laven J, Velez J, Lambert A, Johnson A . Genetic and serologic properties of Zika virus associated with an epidemic, Yap State, Micronesia, 2007. Emerg Infect Dis. 2008; 14(8):1232-9. PMC: 2600394. DOI: 10.3201/eid1408.080287. View

18.

Faria N, Quick J, Claro I, Theze J, de Jesus J, Giovanetti M . Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature. 2017; 546(7658):406-410. PMC: 5722632. DOI: 10.1038/nature22401. View

19.

Quick J, Grubaugh N, Pullan S, Claro I, Smith A, Gangavarapu K . Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc. 2017; 12(6):1261-1276. PMC: 5902022. DOI: 10.1038/nprot.2017.066. View

20.

Danecek P, Bonfield J, Liddle J, Marshall J, Ohan V, Pollard M . Twelve years of SAMtools and BCFtools. Gigascience. 2021; 10(2). PMC: 7931819. DOI: 10.1093/gigascience/giab008. View