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. 2018 Mar;90(3):412-420.
doi: 10.1002/jmv.24984. Epub 2017 Nov 11.

Metagenomic analysis of viral diversity in respiratory samples from patients with respiratory tract infections in Kuwait

Nada Madi  1 , Widad Al-Nakib  1 , Abu Salim Mustafa  1 , Nazima Habibi  2
Affiliations

Metagenomic analysis of viral diversity in respiratory samples from patients with respiratory tract infections in Kuwait

Nada Madi et al. J Med Virol. 2018 Mar.

Abstract

A metagenomic approach based on target independent next-generation sequencing has become a known method for the detection of both known and novel viruses in clinical samples. This study aimed to use the metagenomic sequencing approach to characterize the viral diversity in respiratory samples from patients with respiratory tract infections. We have investigated 86 respiratory samples received from various hospitals in Kuwait between 2015 and 2016 for the diagnosis of respiratory tract infections. A metagenomic approach using the next-generation sequencer to characterize viruses was used. According to the metagenomic analysis, an average of 145, 019 reads were identified, and 2% of these reads were of viral origin. Also, metagenomic analysis of the viral sequences revealed many known respiratory viruses, which were detected in 30.2% of the clinical samples. Also, sequences of non-respiratory viruses were detected in 14% of the clinical samples, while sequences of non-human viruses were detected in 55.8% of the clinical samples. The average genome coverage of the viruses was 12% with the highest genome coverage of 99.2% for respiratory syncytial virus, and the lowest was 1% for torque teno midi virus 2. Our results showed 47.7% agreement between multiplex Real-Time PCR and metagenomics sequencing in the detection of respiratory viruses in the clinical samples. Though there are some difficulties in using this method to clinical samples such as specimen quality, these observations are indicative of the promising utility of the metagenomic sequencing approach for the identification of respiratory viruses in patients with respiratory tract infections.

Keywords: RNA extraction; human metapneumovirus; influenza virus; research and analysis methods; respiratory syncytial virus.

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Figures

Figure 1
Figure 1
Clustered Bar chart of the percentage of patients positive for respiratory viruses detected by multiplex RT‐PCR assay (n = 86)
Figure 2
Figure 2
Pie chart of the taxonomic distribution of metagenomic sequencing reads from clinical samples. Data are average values of reads
Figure 3
Figure 3
Clustered Bar chart of the percentage of patients positive for viruses detected by metagenomic sequencing assay (n = 86)
See this image and copyright information in PMC

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