Last updated: 2021 Sep 29
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A patient with co-infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus showed signs of pneumonia. However, the upper respiratory samples were negative in the SARS-CoV-2 RT-PCR test. Metagenomic next-generation sequencing (mNGS) using bronchoalveolar lavage fluid was used to confirm the presence of SARS-CoV-2. A 69- year old patient had fever and dry cough. CT scan of lungs showed ground-glass opacity in the lower right lung. Multiple nasopharyngeal samples were negative for SARS-CoV-2 by RT-PCR but positive for influenza A. A week later the pateint still complained of persistent fever and shortness of breath. Bronchoalveloar lavage samples were then obtained for metagenomic next generation sequencing. Out of the 3,460 sequences, 99.8% identity and covered 98.69% of the SARS-CoV-2 genome NC_045512.2|SARS-CoV-2|Wuhan-Hu-1 (GenBank accession no. NC_045512.2). Co-infection with other viruses may result in false negative test for COVID-19 in upper respiratory specimens.
(Emerg Infect Dis)
Date of Publishing: 2020 Jun
Title Co-infection with SARS-CoV-2 and Influenza A Virus in Patient with Pneumonia, China
Author(s) nameWu X, Cai Y et al.
Journal Emerg Infect Dis
Impact factor
Citation count: 119
Date of Entry 2021 Sep 29

Metagenomics analysis of three samples from Taiwan revealed the co-existence of Haemophilus parainfluenzae with SARS-CoV-2-positive cases. NGS depths representing exixtence of infections: Haemophilus parainfluenzae (accession number CP035368.2) was the dominant population in metagenomic contigs of CGMH-CGU-07 and -08 samples.
(Emerg Microbes Infect)
Date of Publishing: 2020 Dec
Title SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East
Author(s) nameGong YN, Tsao KC et al.
Journal Emerg Microbes Infect
Impact factor
Citation count: 22

Metagenomics sequencing revealed bacterial and viral co-infections and the respiratory microbial diversity associated with SARS-CoV-2, is a cause of disease severity. SARS-CoV-2 was detected in 31/40 (77.5%) samples positive by RT-PCR. No fungal or protist coinfections were detected
Date of Publishing: 2020 Nov 20
Title Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients
Author(s) nameMostafa HH, Fissel JA et al.
Journal mBio
Impact factor
Citation count: 2

Metagenomics analysis of the first SARS-CoV-2 patient from Ecuador revealed the presence of pathogenic bacterial co-infection. It was most likely involved in worsening the patient's health condition. The Age of patient 50 years, gender: male, Number of DNA sequences were: 206111 Number of Bases: 43603091 Coronavirus sequences represented 0.036%, Of all microorganisms presents.
Date of Publishing: 2020 Jun 14
Title Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador
Author(s) nameMarquez S, Prado-Vivar B et al.
Journal medRxiv
Impact factor
Cant find
Citation count: 1

Metagenomic Analysis of a Sample (WIV04) from Wuhan, China, revealed a new coronavirus (2019-nCoV). It caused an epidemic of acute respiratory syndrome in humans. Of the obtained total reads (10,038,758), 1,582 reads were retained after removing the reads from the human genome. Of which, 1,378 (87.1%) sequences matched the sequence of SARSr-CoV
Date of Publishing: 2020 Mar
Title A pneumonia outbreak associated with a new coronavirus of probable bat origin
Author(s) nameZhou P, Yang XL et al.
Journal Nature
Impact factor
Citation count: 6926