Pathogens that Cause Illness Clinically Indistinguishable from Lassa Fever, Nigeria, 2018

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Abstract

During the 2018 Lassa fever outbreak in Nigeria, samples from patients with suspected Lassa fever but negative Lassa virus PCR results were processed through custom gene expression array cards and metagenomic sequencing. Results demonstrated no single etiology, but bacterial and viral pathogens (including mixed co-infections) were detected.

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Most cited references 7

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Fast and accurate long-read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2010)

Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.sourceforge.net Contact: rd@sanger.ac.uk

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Improved metagenomic analysis with Kraken 2

Derrick E Wood, Jennifer Lu, Ben Langmead (2019)

Although Kraken’s k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold. Kraken 2 also introduces a translated search mode, providing increased sensitivity in viral metagenomics analysis.

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Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

L. Kafetzopoulou, S. Pullan, P. Lemey … (2019)

The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.

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Author and article information

Journal

Journal ID (nlm-ta): Emerg Infect Dis

Journal ID (iso-abbrev): Emerg Infect Dis

Journal ID (publisher-id): EID

Title: Emerging Infectious Diseases

Publisher: Centers for Disease Control and Prevention

ISSN (Print): 1080-6040

ISSN (Electronic): 1080-6059

Publication date (Print): May 2022

Volume: 28

Issue: 5

Pages: 994-997

Affiliations

[1]Public Health England, London, UK (J.W. Ashcroft, H. Bagnall, B. Gannon);

[2]London School of Hygiene and Tropical Medicine, London (J.W. Ashcroft, H. Bagnall, B. Gannon);

[3]Nigeria Centre for Disease Control, Abuja, Nigeria (A. Olayinka, N. Ndodo, C. Dan Nwafor, K. Madubuike, A.S. Musa, A. Ahmad, A. Akinpelu, A. Adeleye, C. Martin, A. Akano, M. Onoja, A. Iniobong, W. Ukponu, C. Arinze, E. Ilori, N. Mba, A. Ahumibe, C. Ihekweazu);

[4]Public Health England, Porton Down, UK (K. Lewandowski);

[5]Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK (M.D. Curran)

Author notes

Address for correspondence: Adebola Olayinka, Nigeria Centre for Disease Control, Plot 801 Ebitu Ukiwe St, Jabi-Abuja, FCT, Nigeria; email: adebola.olayinka@ 123456ncdc.gov.ng

Article

Publisher ID: 21-1153

DOI: 10.3201/eid2805.211153

PMC ID: 9045454

PubMed ID: 35226800

SO-VID: 44e4b910-de49-464d-b07c-ff5360ac8c4d

License:

Preventing Chronic Disease is a publication of the U.S. Government. This publication is in the public domain and is therefore without copyright. All text from this work may be reprinted freely. Use of these materials should be properly cited.

Pathogens that Cause Illness Clinically Indistinguishable from Lassa Fever, Nigeria, 2018

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Abstract

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IOP Publishing: Coronavirus

Most cited references 7

Fast and accurate long-read alignment with Burrows–Wheeler transform

Improved metagenomic analysis with Kraken 2

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

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