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Metagenomics
Last updated: 2021 Sep 29
Total hit(s): 5
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Original Article
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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.
✍
32160148
(
Emerg Infect Dis
)
PMID
32160148
Date of Publishing
: 2020 Jun
Title
Co-infection with SARS-CoV-2 and Influenza A Virus in Patient with Pneumonia, China
Author(s) name
Wu X, Cai Y et al.
Journal
Emerg Infect Dis
Impact factor
6.81
Citation count
: 144
Date of Entry
2021 Sep 29
×
NLM format
Wu X, Cai Y, Huang X, Yu X, Zhao L, Wang F, Li Q, Gu S, Xu T, Li Y, Lu B, Zhan Q. Co-infection with SARS-CoV-2 and Influenza A Virus in Patient with Pneumonia, China. Emerg Infect Dis. 2020 Jun;26(6):1324-1326. PMID:32160148
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: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7473175/bin/TEMI_A_1782271_SM4509.jpg Haemophilus parainfluenzae (accession number CP035368.2) was the dominant population in metagenomic contigs of CGMH-CGU-07 and -08 samples.
✍
32543353
(
Emerg Microbes Infect
)
PMID
32543353
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) name
Gong YN, Tsao KC et al.
Journal
Emerg Microbes Infect
Impact factor
5.84
Citation count
: 69
×
NLM format
Gong YN, Tsao KC, Hsiao MJ, Huang CG, Huang PN, Huang PW, Lee KM, Liu YC, Yang SL, Kuo RL, Chen KF, Liu YC, Huang SY, Huang HI, Liu MT, Yang JR, Chiu CH, Yang CT, Chen GW, Shih SR. SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Emerg Microbes Infect. 2020 Dec;9(1):1457-1466. PMID:32543353
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
✍
33219095
(
mBio
)
PMID
33219095
Date of Publishing
: 2020 Nov 20
Title
Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients
Author(s) name
Mostafa HH, Fissel JA et al.
Journal
mBio
Impact factor
6.5
Citation count
: 39
×
NLM format
Mostafa HH, Fissel JA, Fanelli B, Bergman Y, Gniazdowski V, Dadlani M, Carroll KC, Colwell RR, Simner PJ. Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients. mBio. 2020 Nov 20;11(6):e01969-20. PMID:33219095
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.
✍
32588004
(
medRxiv
)
PMID
32588004
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) name
Marquez S, Prado-Vivar B et al.
Journal
medRxiv
Impact factor
- n/a -
Citation count
: 1
×
NLM format
Marquez S, Prado-Vivar B, Guadalupe JJ, Gutierrez Granja B, Jibaja M, Tobar M, Mora F, Gaviria J, Garcia M, Ligna E, Espinosa F, Reyes J, Barragan V, Rojas-Silva P, Trueba G, Grunauer M, Cardenas P. Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador. medRxiv. 2020 Jun 14:2020.06.11.20128330. PMID:32588004
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
✍
32015507
(
Nature
)
PMID
32015507
Date of Publishing
: 2020 Mar
Title
A pneumonia outbreak associated with a new coronavirus of probable bat origin
Author(s) name
Zhou P, Yang XL et al.
Journal
Nature
Impact factor
24.36
Citation count
: 8438
×
NLM format
Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020 Mar;579(7798):270-273. PMID:32015507