Rapid viral- and microbial diagnosing, tropical disease screening

Differentiating between infectious and non-infectious illness, and identifying the underlying etiology of infection, can be quite challenging. For example, more than half of cases of encephalitis remain undiagnosed, despite extensive testing using state-of-the-art clinical laboratory methods. Metagenomic sequencing shows promise as a sensitive (as few as one read depth) and rapid method to diagnose infection by comparing DNA found in a patient's sample to the latest non-redundant database of NCBI.


Case study 1.

Powassan virus and metagenomic sequencing reads from human clinical cerebrospinal fluid sample: reanalyzing NCBI project PRJNA398476, sample SRX3104228

Merged bam file from three independent libraries POWV_M030T_CSF.l1 (sequenced on two separate MiSeq runs AVFHP.1 and AYYCK.1, two separate HiSeq runs BHCGN.1 and HC53H.1, and a third HiSeq run after hybrid capture HC53H.2), POWV_M030T_CSF.l2 (sequenced on three separate MiSeq runs AW5DT.1 AYCW9.1 and AYYCK.1.2, one HiSeq run HC53H.1.6, and a second HiSeq run after hybrid capture HC53H.2.9), and POWV_M030T.l3 (sequenced on one MiSeq run AYYCK.1.3, one HiSeq run HC53H.1.7, and one HiSeq run after hybrid capture HC53H.2). Libraries have been cleaned of human reads.
Figure 1. Seqomics' reanalysis confirms encephalitis (Powassan) virus presence and shows significant HIV and herpesvirus co-occurrence


SRR5945841.daa (results in MEGAN6 compatible file, please extract with WinRAR)


Case study 2.

Southampton Asthma metagenomics: reanalyzing EBI project ERP006003, sample ERR525606

55 subjects underwent detailed clinical and immunological phenotyping, sputum induction and bronchoscopy during periods of clinical stability. In addition to 15 healthy controls, 9 mild, 16 moderate and 15 severe ashthmatics (without bronchiectasis) were included. Protected bronchoalveolar lavage (BAL) and induced symptoms were analysed by WGS for RNA and DNA from bacterial, viral and fungal genomes. 88 samples were sequenced using 454 FLX Titanium. Single end library. Data were provided as fasta files following adapter trimming.


Figure 2. Analysis reveals massive amounts of Streptococcus and Prevotella related sequences


S106.daa (results in MEGAN6 compatible file)

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