Respiratory Co-Infections: Modulators of SARS-CoV-2 Patients' Clinical Sub-Phenotype.

Frontiers in Microbiology
Priyanka MehtaRajesh Pandey

Abstract

Co-infection with ancillary pathogens is a significant modulator of morbidity and mortality in infectious diseases. There have been limited reports of co-infections accompanying SARS-CoV-2 infections, albeit lacking India specific study. The present study has made an effort toward elucidating the prevalence, diversity and characterization of co-infecting respiratory pathogens in the nasopharyngeal tract of SARS-CoV-2 positive patients. Two complementary metagenomics based sequencing approaches, Respiratory Virus Oligo Panel (RVOP) and Holo-seq, were utilized for unbiased detection of co-infecting viruses and bacteria. The limited SARS-CoV-2 clade diversity along with differential clinical phenotype seems to be partially explained by the observed spectrum of co-infections. We found a total of 43 bacteria and 29 viruses amongst the patients, with 18 viruses commonly captured by both the approaches. In addition to SARS-CoV-2, Human Mastadenovirus, known to cause respiratory distress, was present in a majority of the samples. We also found significant differences of bacterial reads based on clinical phenotype. Of all the bacterial species identified, ∼60% have been known to be involved in respiratory distress. Among the co-pathogen...Continue Reading

References

Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Jan 11, 2011·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Sumit R MajumdarThomas J Marrie
May 17, 2013·Journal of the Royal Society, Interface·R YaariL Stone
Mar 4, 2014·Genome Biology·Derrick E Wood, Steven L Salzberg
Oct 4, 2014·Emerging Infectious Diseases·Parvaiz A KoulRenu B Lal
Mar 10, 2015·Nature Methods·Daehwan KimSteven L Salzberg
Mar 24, 2016·Methods in Molecular Biology·Florian Hahne, Robert Ivanek
May 19, 2016·Emerging Infectious Diseases·Magdalena Kendall ScottAnn Thomas
Feb 7, 2018·Frontiers in Cellular and Infection Microbiology·Rebekah M Martin, Michael A Bachman
Jun 1, 2018·Case Reports in Infectious Diseases·Foula VassilaraAntonios Papadopoulos
Apr 28, 2019·Nucleic Acids Research·Frédéric LemoineOlivier Gascuel
Sep 26, 2019·Bioinformatics·Florian P Breitwieser, Steven L Salzberg
Feb 8, 2020·JAMA : the Journal of the American Medical Association·Dawei WangZhiyong Peng
Mar 9, 2020·The Lancet. Respiratory Medicine·Silvio A Ñamendys-Silva
Mar 12, 2020·Emerging Infectious Diseases·Xiaojing WuQingyuan Zhan
Mar 15, 2020·Science China. Life Sciences·Dachuan LinKaisong Huang
Apr 16, 2020·JAMA : the Journal of the American Medical Association·David KimIan Brown
Apr 23, 2020·JAMA : the Journal of the American Medical Association·Safiya RichardsonTheodoros P Zanos
May 15, 2020·Virus Research·Xiaojuan ZhuLunbiao Cui
Jun 5, 2020·Journal of Medical Virology·Resat OzarasSuat Bilir
Jul 17, 2020·Clinical Autonomic Research : Official Journal of the Clinical Autonomic Research Society·Alejandra González-Duarte, Lucy Norcliffe-Kaufmann
Jul 28, 2020·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·Bradley J LangfordNick Daneman
Jul 30, 2020·Respiratory Research·Sebastiaan DhontBart N Lambrecht
Sep 10, 2020·BMJ Case Reports·Atanu ChandraParthasarathi Karmakar
Sep 29, 2020·Frontiers in Microbiology·Bill W MasseyHerbert Y Meltzer
Oct 1, 2020·Wellcome Open Research·Pramod KumarPartha Rakshit
Oct 28, 2020·Nature·Jessica A PlantePei-Yong Shi
Dec 22, 2020·Case Reports in Pulmonology·Chaitanya PalNikhil Madan

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Software Mentioned

Seq
FastQC
Trim Galore
PhyML
R corrplot
Pavian
Holo
FIGTREE
Nextclade
Nextflow

Related Concepts

Related Feeds

Botulism (ASM)

Botulism is a rare but serious paralytic illness caused by a nerve toxin that is produced by the bacterium clostridium botulinum. Discover the latest research on botulism here.

Botulism

Botulism is a rare but serious paralytic illness caused by a nerve toxin that is produced by the bacterium clostridium botulinum. Discover the latest research on botulism here.

Bacillus Cereus Infection

Bacillus Cereus is a gram-positive bacteria that is the cause of some foodborne illnesses and leads to diarrhea and vomiting. Discover the latest research on Bacillus Cereus Infection here.

Related Papers

Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America
Aniruddha HazraJessica Ridgway
© 2021 Meta ULC. All rights reserved