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Using metagenomic sequencing to evaluate the composition of microbiome in patients with Covid-19


Metagenomic Next-Generation Sequencing (mNGS) combines the offer of detection of early stages of emerging pathogens directly from clinical specimens and provides information on the microbiome composition of the patient. The latter provides a snapshot of the patient’s microbiome, offering valuable insight into possible co-infections that may be associated with disease progression and prognosis. Growing evidence has been found that the microbiome of the respiratory tract can have an impact on the health and disease progression in patients, but most research has been focused on the interactions between different strains of bacteria. With that in mind, it may be possible to predict which patients are more likely to develop severe disease by analysing their microbiome.

Previously, most of the studies of the SARS-CoV-2 co-infections focused on using real-time reverse transcription-PCR (RT-PCR) to detect co-infections, which carried a problem of heterogeneity among the detection methodology used between the studies. A study by Mostafa et al. (Mostafa et al., 2020) evaluated the use of mNGS (specifically direct long-read metatranscriptomic and metagenomic sequencing) for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from nasopharyngeal (NS) swabs in 50 patients under investigation for CoV disease 2019 (COVID-19). They observed high viral burdens (i.e. low cycle threshold (Ct) values) in the samples, which made it possible to obtain enough sequencing reads without the need for viral enrichment or amplification. Furthermore, the method shows the dynamic of the viral load in the nasopharynx, with a higher load in the early stages of the disease which progressively wanes as the disease progresses. Additionally, the researchers detected a reduction of the microbiome in COVID-19-positive patients and statistically significant shifts in the microbiome between COVID-19-positive and -negative patients, with the latter having a higher quantity of Propionibacteriaceae and a lower quantity of Corynebacterium accolens.


Mostafa, H. H. et al. (2020) ‘Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients’, mBio. Edited by S. M. Leal and P. Gilligan, 11(6), pp. 1–13. doi: 10.1128/mBio.01969-20.

Dr Nina Fajs

Clinical Scientist, Edinburgh Genetics


Image by Muhammad Syafi Al - adam


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