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Respiratory Co-Infections: Modulators of SARS-CoV-2 Patients' Clinical Sub-Phenotype.
Mehta, Priyanka; Sahni, Shweta; Siddiqui, Samreen; Mishra, Neha; Sharma, Pooja; Sharma, Sachin; Tyagi, Akansha; Chattopadhyay, Partha; Vivekanand, A; Devi, Priti; Khan, Azka; Waghdhare, Swati; Budhiraja, Sandeep; Uppili, Bharathram; Maurya, Ranjeet; Nangia, Vivek; Shamim, Uzma; Hazarika, Pranjal P; Wadhwa, Saruchi; Tyagi, Nishu; Dewan, Arun; Tarai, Bansidhar; Das, Poonam; Faruq, Mohammed; Agrawal, Anurag; Jha, Sujeet; Pandey, Rajesh.
  • Mehta P; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Sahni S; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Siddiqui S; Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, New Delhi, India.
  • Mishra N; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Sharma P; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Sharma S; Academy of Scientific and Innovative Research, Ghaziabad, India.
  • Tyagi A; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Chattopadhyay P; Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, New Delhi, India.
  • Vivekanand A; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Devi P; Academy of Scientific and Innovative Research, Ghaziabad, India.
  • Khan A; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Waghdhare S; Academy of Scientific and Innovative Research, Ghaziabad, India.
  • Budhiraja S; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Uppili B; Academy of Scientific and Innovative Research, Ghaziabad, India.
  • Maurya R; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Nangia V; Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, New Delhi, India.
  • Shamim U; Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, New Delhi, India.
  • Hazarika PP; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Wadhwa S; Academy of Scientific and Innovative Research, Ghaziabad, India.
  • Tyagi N; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Dewan A; Academy of Scientific and Innovative Research, Ghaziabad, India.
  • Tarai B; Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, New Delhi, India.
  • Das P; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Faruq M; Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, New Delhi, India.
  • Agrawal A; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
  • Jha S; Academy of Scientific and Innovative Research, Ghaziabad, India.
  • Pandey R; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
Front Microbiol ; 12: 653399, 2021.
Article in English | MEDLINE | ID: covidwho-1389208
Semantic information from SemMedBD (by NLM)
1. Pathogenic organism ASSOCIATED_WITH Communicable Diseases
Subject
Pathogenic organism
Predicate
ASSOCIATED_WITH
Object
Communicable Diseases
2. Coinfection COEXISTS_WITH COVID-19
Subject
Coinfection
Predicate
COEXISTS_WITH
Object
COVID-19
3. Tract PART_OF Nasopharynx
Subject
Tract
Predicate
PART_OF
Object
Nasopharynx
4. Tract PART_OF Patients
Subject
Tract
Predicate
PART_OF
Object
Patients
5. Virus PROCESS_OF Patients
Subject
Virus
Predicate
PROCESS_OF
Object
Patients
6. Mastadenovirus PROCESS_OF Homo sapiens
Subject
Mastadenovirus
Predicate
PROCESS_OF
Object
Homo sapiens
7. Bacteri ASSOCIATED_WITH C0476273
Subject
Bacteri
Predicate
ASSOCIATED_WITH
Object
C0476273
8. Pathogenic organism ASSOCIATED_WITH Communicable Diseases
Subject
Pathogenic organism
Predicate
ASSOCIATED_WITH
Object
Communicable Diseases
9. Coinfection COEXISTS_WITH COVID-19
Subject
Coinfection
Predicate
COEXISTS_WITH
Object
COVID-19
10. Tract PART_OF Nasopharynx
Subject
Tract
Predicate
PART_OF
Object
Nasopharynx
11. Tract PART_OF Patients
Subject
Tract
Predicate
PART_OF
Object
Patients
12. Virus PROCESS_OF Patients
Subject
Virus
Predicate
PROCESS_OF
Object
Patients
13. Mastadenovirus PROCESS_OF Homo sapiens
Subject
Mastadenovirus
Predicate
PROCESS_OF
Object
Homo sapiens
14. Bacteria, Anaerobic ASSOCIATED_WITH Respiratory distress
Subject
Bacteria, Anaerobic
Predicate
ASSOCIATED_WITH
Object
Respiratory distress
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-pathogens present in our sample cohort, anaerobic bacteria accounted for a preponderance of bacterial diversity with possible role in respiratory distress. Clostridium botulinum, Bacillus cereus and Halomonas sp. are anaerobes found abundantly across the samples. Our findings highlight the significance of metagenomics based diagnosis and detection of SARS-CoV-2 and other respiratory co-infections in the current pandemic to enable efficient treatment administration and better clinical management. To our knowledge this is the first study from India with a focus on the role of co-infections in SARS-CoV-2 clinical sub-phenotype.
Keywords

Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study / Risk factors Language: English Journal: Front Microbiol Year: 2021 Document Type: Article Affiliation country: FMICB.2021.653399

Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study / Risk factors Language: English Journal: Front Microbiol Year: 2021 Document Type: Article Affiliation country: FMICB.2021.653399